Genes and uses for plant improvement

ABSTRACT

This invention provides transgenic plant cells with recombinant DNA for expression of proteins that are useful for imparting enhanced agronomic trait(s) to transgenic crop plants. This invention also provides transgenic plants and progeny seed comprising the transgenic plant cells where the plants are selected for having an enhanced trait selected from the group of traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Also disclosed are methods for manufacturing transgenic seed and plants with enhanced traits.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims benefit under 35USC § 119(e) of U.S. provisional application Ser. No. 60/642,717, filed Jan. 12, 2005, herein incorporated by reference.

INCORPORATION OF SEQUENCE LISTING

Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-ROMs, each containing the file named 38-21(53629)B_seqListing.txt, which is 59,207,680 bytes (measured in MS-WINDOWS) and was created on Jan. 11, 2006, are herein incorporated by reference.

INCORPORATION OF COMPUTER PROGRAM LISTING

Computer Program Listing folders hmmer-2.3.2 and 158pfamDir are contained on a compact disc and is hereby incorporated herein by reference in their entirety. Folder hmmer-2.3.2 contains the source code and other associated file for implementing the HMMer software for Pfam analysis. Folder 158pfamDir contains 158 Pfam Hidden Markov Models. Both folders were created on the disk on Jan. 11, 2006, having a total size of 16,027,648 bytes (measured in MS-WINDOWS).

FIELD OF THE INVENTION

Disclosed herein are inventions in the field of plant genetics and developmental biology. More specifically, the present inventions provide transgenic seeds for crops, wherein the genome of said seed comprises recombinant DNA, the expression of which results in the production of transgenic plants that have improved trait(s).

BACKGROUND OF THE INVENTION

Transgenic plants with improved traits such as improved yield, environmental stress tolerance, pest resistance, herbicide tolerance, modified seed compositions, and the like are desired by both farmers and consumers. Although considerable efforts in plant breeding have provided significant gains in desired traits, the ability to introduce specific DNA into plant genomes provides further opportunities for generation of plants with improved and/or unique traits. The ability to develop transgenic plants with improved traits depends in part on the identification of genes that are useful in recombinant DNA constructs for production of transformed plants with improved properties.

SUMMARY OF THE INVENTION (NEW)

This invention provides recombinant DNA for expression of proteins that impart enhanced agronomic traits in transgenic plants. Recombinant DNA in this invention is provided in a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein having at least one amino acid domain in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam domain names identified in Table 17. In more specific embodiments of the invention plant cells are provided which express a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of consensus amino acid sequences consisting of the consensus amino acid sequence constructed for SEQ ID NO: 205 and homologs thereof listed in Table 2 through the consensus amino acid sequence constructed for SEQ ID NO:408 and homologs thereof listed in Table 2. Amino acid sequences of homologs are SEQ ID NO:409 through 19247. In even more specific embodiments of the invention the protein expressed in plant cells is a protein selected from the group of proteins identified in Table 1 by annotation to a related protein in Genbank and alternatively identified in Table 16 by identification of protein domain family. An exemplary plant cell of this invention has recombinant DNA that encodes a protein identified by the Pdam name “RNA_pol_L”.

Other aspects of the invention are specifically directed to transgenic plant cells comprising the recombinant DNA of the invention, transgenic plants comprising a plurality of such plant cells, progeny transgenic seed, embryo and transgenic pollen from such plants. Such plant cells are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA and that express the protein by screening transgenic plants in the population for an enhanced trait as compared to control plants that do not have said recombinant DNA, where the enhanced trait is enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced tolerance to salt exposure, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Thus, this invention provides transgenic plants and seeds with cells having recombinant DNA that impart at least one of those enhanced traits to the plants or seeds.

In yet another aspect of the invention the plant cells, plants, seeds, embryo and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell. Such tolerance is especially useful not only as an advantageous trait in such plants but is also useful in a selection step in the methods of the invention. In aspects of the invention the agent of such herbicide is a glyphosate, dicamba, or glufosinate compound.

Yet other aspects of the invention provide transgenic plants which are homozygous for the recombinant DNA and transgenic seed of the invention from corn, soybean, cotton, canola, alfalfa, wheat or rice plants. In other important embodiments for practice of various aspects of the invention in Argentina the recombinant DNA is provided in plant cells derived from corn lines that that are and maintain resistance to the Mal de Rio Cuarto virus or the Puccina sorghi fungus or both.

This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA for expressing a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names identified in Table 17. More specifically the method comprises (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA, (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants, (c) verifying that the recombinant DNA is stably integrated in said selected plants, (d) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by nucleotides in a sequence of one of SEQ ID NO:1-204; and (e) collecting seed from a selected plant. In one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention the plants are selected by identifying plants with the enhanced trait. The methods are especially useful for manufacturing corn, soybean, cotton, alfalfa, wheat or rice seed selected as having one of the enhanced traits described above.

Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names identified in Table 17. The methods further comprise producing corn plants from said hybrid corn seed, where a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.

Another aspect of the invention provides a method of selecting a plant comprising plant cells of the invention by using an immunoreactive antibody to detect the presence of protein expressed by recombinant DNA in seed or plant tissue. Yet another aspect of the invention provides anti-counterfeit milled seed having, as an indication of origin, a plant cells of this invention with unique recombinant DNA.

Another aspect of the invention provides plant cells having recombinant DNA for suppressing the expression of DNA identified in Table 1 and Table 16. More specific aspects of the invention provide plant cells having recombinant DNA for suppressing the expression of a protein having the function in a plant of the protein with amino acid sequence of SEQ ID NO: 213, 215, 218, 222, 258, 269, 275, 334, 361, 368, and 407 or the corresponding Pfam identified in Table 16, i.e. Catalase, Bromdomain, FTCD_N, MatE, DPBB_(—)1, tRNA-synt_(—)2b, Sugar_tr and MFS_(—)1, DUF6 and DUF250, LEA_(—)4, MIP and DUF231, respectively. Such suppression can be effected by any of a number of ways known in the art, e.g. anti-sense suppression, sense co-suppression, RNAi or knockout.

Still other specific aspects of this invention relate to growing transgenic plants with enhanced water use efficiency or enhanced nitrogen use efficiency. For instance, this invention provides methods of growing a corn, cotton or soybean crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency. Alternatively methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop. This invention also provides methods of growing a corn, cotton or soybean crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.

The various aspects of this invention are especially useful for transgenic plant cells in seeds and transgenic plants having any of the above-described enhanced traits in crop plants such as corn (maize), soybean, cotton, canola (rape), wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.

The invention also comprises recombinant DNA constructs of the DNA useful for imparting enhanced traits in plants having three cells of this invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an alignment of amino acid sequences.

FIGS. 2 and 3 are plasmid maps.

DETAILED DESCRIPTION OF THE INVENTION

In the attached sequence listing:

SEQ ID NO: 1-204 are DNA sequence of “genes” used in the recombinant DNA imparting an enhanced trait in plant cells;

SEQ ID NO:205-408 are amino acid sequence of the cognate protein of those “genes”;

SEQ ID NO:409-19247 are amino acid sequence of homologous proteins;

SEQ ID NO: 19248 is a consensus amino acid sequence.

SEQ ID NO: 19249 is a DNA sequence of a plasmid vector useful for corn transformation; and

SEQ ID NO: 19250 is a DNA sequence of a plasmid vector useful for soybean transformation.

As used herein, “gene” means DNA including chromosomal DNA, plasmid DNA, cDNA, synthetic DNA, or other DNA that is transcribed to RNA, e.g. mRNA that encodes a protein or a protein fragment or anti-sense RNA or dsRNA for suppression of expression of a target gene and its cognate protein.

“Transgenic plant cell” means a plant cell produced as an original transformation event, cells in plants regenerated from the original transformation, cells in progeny plants and seeds, and cells in plants and seed from later generations or crosses of progeny plants and seeds, where such plant cells have recombinant DNA in their genome resulting from the original transformation.

“Recombinant DNA” means genetically engineered polynucleotide produced from endogenous and/or exogenous elements generally arranged as a transcription unit. Recombinant DNA may comprise DNA segments obtained from different sources, or DNA segments obtained from the same source, but which have been manipulated to join DNA segments which do not naturally exist in the joined form. A recombinant polynucleotide may exist outside of the cell, for example as a PCR fragment, or integrated into a genome, such as a plant genome.

“Trait” means to a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell. In some instances, this characteristic is visible to the human eye, such as seed or plant size, or can be measured by biochemical techniques, such as detecting the protein, starch, or oil content of seed or leaves, or by observation of a metabolic or physiological process, e.g. by measuring uptake of carbon dioxide, or by the observation of the expression level of a gene or genes, e.g., by employing Northern analysis, RT-PCR, microarray gene expression assays, or reporter gene expression systems, or by agricultural observations such as stress tolerance, yield, or pathogen tolerance. An “enhanced trait” as used in describing the aspects of this invention includes enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced shade tolerance, enhanced tolerance to salt exposure, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

As used herein, “control plant” is a plant without trait-improving recombinant DNA. A control plant is used to measure and compare trait improvement in a transgenic plant with such trait-improving recombinant DNA. A suitable control plant may be a non-transgenic plant of the parental line used to generate a transgenic plant herein. Alternatively, a control plant may be a transgenic plant that comprises an empty vector or marker gene, but does not contain the recombinant DNA that produces the trait improvement. A control plant may also be a negative segregant progeny of hemizygous transgenic plant. In certain demonstrations of trait improvement, the use of a limited number of control plants can cause a wide variation in the control dataset. In analyzing trait data during screening to discover DNA useful in the plant cells of this invention it is useful to minimize the effect of the variation within the control dataset, i.e. a “reference” which is a trimmed mean of all data from both transgenic and control plants grown under the same conditions and at the same developmental stage. The trimmed mean is calculated by eliminating a specific percentage, i.e. 20%, of the smallest and largest observation from the data set and then calculating the average of the remaining observation. Many transgenic plants comprising transgenic plant cells containing the recombinant DNA identified herein as imparting an enhanced trait will not exhibit an enhanced agronomic trait. The transgenic plants and seeds comprising the transgenic plant cells and having enhanced agronomic traits of this invention are identified by screening a population of transgenic plants and/or seeds for the members of the population having the enhanced trait. Screens for transgenic plant cells in crop plants are described more particularly in the examples below. In some cases, the trait enhancement can be measured quantitatively. For example, the trait enhancement can be at least a 2% desirable difference in an observed trait, at least a 5% desirable difference, at least about a 10% desirable difference, at least about a 20% desirable difference, at least about a 30% desirable difference, at least about a 50% desirable difference, at least about a 70% desirable difference, or at least about a 100% difference, or an even greater desirable difference. In other cases, the trait enhancement is measured qualitatively.

Many agronomic traits can affect “yield”, including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Other traits that can affect yield include, efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill. Also of interest is the generation of transgenic plants that demonstrate desirable phenotypic properties that may or may not confer an increase in overall plant yield. Such properties include enhanced plant morphology, plant physiology or improved components of the mature seed harvested from the transgenic plant.

“Stress condition” refers to the condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development. A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield. Specifically, “water deficit stress” used herein preferably refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which may result in water deficit stress include heat, drought, high salinity and PEG induced osmotic stress. “Cold stress” used herein preferably refers to the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant. “Low nitrogen availability stress” used herein preferably refers to a plant growth condition with 50% of the conventional nitrogen inputs. “Shade stress” used herein preferably refers to limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress may become exacerbated when the planting density exceeds the average prevailing density for a particular plant species. The average prevailing densities per acre of a few examples of crop plants in the USA in the year 2000 were: wheat 1,000,000-1,500,000; rice 650,000-900,000; soybean 150,000-200,000, canola 260,000-350,000, sunflower 17,000-23,000 and cotton 28,000-55,000 plants per acre (Cheikh, et al., (2003) U.S. Patent Application No. 20030101479).

“Increased yield” of a transgenic plant of the present invention may be evidenced and measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tons per acre, tons per acre, kilo per hectare. For example, maize yield may be measured as production of shelled corn kernels per unit of production area, e.g. in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, e.g. at 15.5% moisture. Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved tolerance to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Trait-enhancing recombinant DNA may also be used to provide transgenic plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways.

“Expression” means transcription of DNA to produce RNA. The resulting RNA may be without limitation mRNA encoding a protein, antisense RNA that is complementary to an mRNA encoding a protein, or an RNA transcript comprising a combination of sense and antisense gene regions, such as for use in RNAi technology. Expression as used herein may also refer to production of encoded protein from mRNA.

“Promoter” means a region of DNA that is upstream from the start of transcription and is involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which comprise genes expressed in plant cells such Agrobacterium or Rhizobium. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters which initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions. As used herein, “antisense orientation” includes reference to a polynucleotide sequence that is operably linked to a promoter in an orientation where the antisense strand is transcribed. The antisense strand is sufficiently complementary to an endogenous transcription product such that translation of the endogenous transcription product is often inhibited. “Operably linked” refers to the association of two or more nucleic acid fragments on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

“Consensus amino acid sequence” means an artificial, amino acid sequence of conserved parts of the proteins encoded by homologous genes, e.g. as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins or a group of proteins having identified by the gathering cutoff for a Pfam protein domain family.

Homologous genes are genes which encode homologous proteins with the same or similar biological function or having the same Pfam protein domain family. Homologous genes may be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.

“Percent identity” refers to the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, e.g. nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100. “% identity to a consensus amino acid sequence” is 100 times the identity fraction in a window of alignment of an amino acid sequence of a test protein optimally aligned to consensus amino acid sequence of this invention.

“Arabidopsis” means plants of Arabidopsis thaliana.

As used herein “Pfam” refers to a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 18.0 (August 2005) contains alignments and models for 7973 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. Pfam is currently maintained and updated by a Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the Pfam alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low. Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins in the same protein family are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Model which characterizes the Pfam domain using HMMER software, a current version of which is provided in the appended computer listing. Candidate proteins meeting the gathering cutoff for the alignment of a particular Pfam are in the protein family and have cognate DNA that is useful in constructing recombinant DNA for the use in the plant cells of this invention. Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein in a common Pfam for recombinant DNA in the plant cells of this invention are also included in the appended computer listing. The HMMER software and Pfam databases are version 18.0 and were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO:205 through SEQ ID NO:408. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 27 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfams for use in this invention, as more specifically disclosed below, are 2-oxoacid_dh, ADH_N, ADH_zinc_N, AP2, AUX_IAA, Aa_trans, Abhydrolase_(—)1, Acyl_transf_(—)1, Aldedh, Aldo_ket_red, Alpha-amylase, Aminotran_(—)1_(—)2, Aminotran_(—)3, Ammonium_transp, Arm, Asn_synthase, BAG, BSD, Beta_elim_lyase, Biotin_lipoyl, Brix, Bromodomain, C1_(—)4, CTP_transf_(—)2, Catalase, CcmH, Chal_sti_synt_C, Cyclin_C, Cyclin_N, Cys_Met_Meta_PP, DAO, DIM1, DPBB_(—)1, DRMBL, DUF167, DUF231, DUF250, DUF6, DUF783, DUF962, E2F_TDP, E3_binding, EBP, Enolase_C, Enolase_N, F420_oxidored, FAD_binding_(—)2, FA_desaturase, FKBP_C, FTCD_N, Fe_bilin_red, Fer4, GAF, GATase_(—)2, GIDA, GSHPx, Gpi16, HGTP_anticodon, HI0933_like, HLH, HMG_CoA_synt, HWE_HK, Hamlp_like, HhH-GPD, Homeobox, Hpt, Iso_dh, K-box, LEA_(—)4, LRRNT_(—)2, LRR_(—)1, Ldh_(—)1_C, Ldh_(—)1_N, Lectin_legA, Lectin_legB, Lipase_GDSL, MFS_(—)1, MIP, MatE, Metalloenzyme, Methyltransf_(—)11, Methyltransf_(—)12, Molybdop_Fe4S4, Molybdopterin, Molydop_binding, Mov34, MtN3_slv, Myb_DNA-binding, NAD_Gly3P_dh_N, NAD_binding_(—)2, NIR_SIR, NIR_SIR_ferr, NPH3, NTP_transferase, Nuc_sug_transp, PA, PAR1, PFK, PGI, PGK, PGM_PMM_(—)1, PGM_PMM_II, PGM_PMM_III, PGM_PMM_IV, PP2C, PTR2, Peptidase_C26, Phi_(—)1, Phytochrome, Pkinase, Pkinase_Tyr, Pollen_allerg_(—)1, Pribosyltran, Proteasome, Pyr_redox, Pyr_redox_(—)2, Pyr_redox_dim, RNA_pol_L, RNA_pol_Rpb6, RRM_(—)1, RRN3, Radical_SAM, Ras, Response_reg, Rhodanese, Ribosomal_S8e, Rieske, SAC3_GANP, SBDS, SET, SRF-TF, SURF5, Skp1, Skp1_POZ, Ssl1, Sterol_desat, Sugar_tr, TCP, ThiF, Transaldolase, UQ_con, Ubie_methyltran, WD40, WRKY, adh_short, bZIP_(—)1, bZIP_(—)2, cNMP_binding, iPGM_N, p450, tRNA-synt_(—)2b, ubiquitin, zf-A20, zf-AN1, zf-B_box, zf-C₂H₂, zf-C3HC4, zf-CCCH, the databases for which are included in the appended computer program listing.

Recombinant DNA Constructs

This invention provides recombinant DNA constructs comprising one or more of the genes disclosed herein for imparting one or more enhanced traits to transgenic plants and seeds. Such constructs also typically comprise a promoter operatively linked to said polynucleotide to provide for expression in a target plant. Other construct components may include additional regulatory elements, such as 5′ or 3′ untranslated regions (such as polyadenylation sites), intron regions, and transit or signal peptides. Such recombinant DNA constructs can be assembled using methods known to those of ordinary skill in the art.

Recombinant constructs prepared in accordance with this invention generally includes a 3′ untranslated DNA region (UTR) that typically contains a polyadenylation sequence following the polynucleotide coding region. Examples of useful 3′ UTRs include those from the nopaline synthase gene of Agrobacterium tumefaciens (nos), a gene encoding the small subunit of a ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcS), and the T7 transcript of Agrobacterium tumefaciens and those 3′ UTR elements disclosed in the following examples. Constructs and vectors may also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides, see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.

Table 1 provides a list of genes that can be used in recombinant DNA for imparting an enhanced trait in the transgenic plant cells, plants and seeds of this invention. In screens of recombinant DNA expressed in a model plant the recombinant DNA was shown to be associated with enhanced traits. The cognate protein was used to identify homologs for constructing a consensus amino acid sequence for each cognate protein and for identifying the characterizing Pfams. With reference to Table 1:

“NUC SEQ ID” refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing;

“PEP SEQ ID” refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein cognate to a particular DNA;

“construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA;

“gene” refers to an arbitrary name used to identify the particular DNA;

“orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter; and

“species name” refers to the organism from which the particular DNA was derived.

TABLE 1 NUC PEP SEQ SEQ ID ID construct_id Gene orientation Species Name 1 205 12360 CGPG1018 SENSE Arabidopsis thaliana 2 206 12030 CGPG1063 SENSE Arabidopsis thaliana 3 207 15210 CGPG1124 SENSE Arabidopsis thaliana 4 208 17465 CGPG1178 SENSE Arabidopsis thaliana 5 209 13222 CGPG1259 SENSE Arabidopsis thaliana 6 210 12919 CGPG1290 SENSE Arabidopsis thaliana 7 211 12927 CGPG1300 SENSE Arabidopsis thaliana 8 212 14841 CGPG1572 SENSE Arabidopsis thaliana 9 213 13478 CGPG1616 ANTI-SENSE Arabidopsis thaliana 10 214 17309 CGPG1840 SENSE Arabidopsis thaliana 11 215 19116 CGPG1861 ANTI-SENSE Arabidopsis thaliana 12 216 14837 CGPG1882 SENSE Arabidopsis thaliana 13 217 71253 CGPG195 SENSE Arabidopsis thaliana 14 218 16004 CGPG2061 ANTI-SENSE Arabidopsis thaliana 15 219 72712 CGPG2256 SENSE Arabidopsis thaliana 16 220 71546 CGPG2305 SENSE Arabidopsis thaliana 17 221 70109 CGPG2368 SENSE Saccharomyces cerevisiae 18 222 10335 CGPG246 ANTI-SENSE Arabidopsis thaliana 19 223 17919 CGPG2780 SENSE Arabidopsis thaliana 20 224 71148 CGPG3225 SENSE Arabidopsis thaliana 21 225 19647 CGPG3229 SENSE Arabidopsis thaliana 22 226 18844 CGPG3371 SENSE Arabidopsis thaliana 23 227 19525 CGPG3548 SENSE Arabidopsis thaliana 24 228 19617 CGPG3573 SENSE Arabidopsis thaliana 25 229 19750 CGPG3913 SENSE Saccharomyces cerevisiae 26 230 19964 CGPG3922 SENSE Glycine max 27 231 19814 CGPG3934 SENSE Glycine max 28 232 19720 CGPG3954 SENSE Glycine max 29 233 19845 CGPG3956 SENSE Glycine max 30 234 71072 CGPG3963 SENSE Glycine max 31 235 19949 CGPG4010 SENSE Glycine max 32 236 19902 CGPG4016 SENSE Glycine max 33 237 19981 CGPG4019 SENSE Glycine max 34 238 19757 CGPG4037 SENSE Glycine max 35 239 19850 CGPG4056 SENSE Glycine max 36 240 19942 CGPG4115 SENSE Glycine max 37 241 19787 CGPG4124 SENSE Glycine max 38 242 19801 CGPG4137 SENSE Glycine max 39 243 19705 CGPG4156 SENSE Glycine max 40 244 19737 CGPG4175 SENSE Glycine max 41 245 19812 CGPG4184 SENSE Glycine max 42 246 71556 CGPG4298 SENSE Arabidopsis thaliana 43 247 71330 CGPG4457 SENSE Arabidopsis thaliana 44 248 71332 CGPG4460 SENSE Arabidopsis thaliana 45 249 71571 CGPG4493 SENSE Arabidopsis thaliana 46 250 70677 CGPG4558 SENSE Arabidopsis thaliana 47 251 71689 CGPG4661 SENSE Glycine max 48 252 73685 CGPG4807 SENSE Arabidopsis thaliana 49 253 72636 CGPG4858 SENSE Arabidopsis thaliana 50 254 73651 CGPG4869 SENSE Arabidopsis thaliana 51 255 73342 CGPG4876 SENSE Arabidopsis thaliana 52 256 73271 CGPG5011 SENSE Arabidopsis thaliana 53 257 73282 CGPG5071 SENSE Arabidopsis thaliana 54 258 10903 CGPG514 ANTI-SENSE Arabidopsis thaliana 55 259 73913 CGPG5337 SENSE Glycine max 56 260 74305 CGPG5400 SENSE Arabidopsis thaliana 57 261 74306 CGPG5402 SENSE Arabidopsis thaliana 58 262 73769 CGPG5430 SENSE Arabidopsis thaliana 59 263 74237 CGPG5448 SENSE Arabidopsis thaliana 60 264 74244 CGPG5466 SENSE Arabidopsis thaliana 61 265 74256 CGPG5491 SENSE Arabidopsis thaliana 62 266 72714 CGPG5513 SENSE Saccharomyces cerevisiae 63 267 16014 CGPG552 SENSE Arabidopsis thaliana 64 268 72751 CGPG5524 SENSE Saccharomyces cerevisiae 65 269 10814 CGPG554 ANTI-SENSE Arabidopsis thaliana 66 270 72743 CGPG5555 SENSE Saccharomyces cerevisiae 67 271 72721 CGPG5569 SENSE Saccharomyces cerevisiae 68 272 72959 CGPG5608 SENSE Glycine max 69 273 72984 CGPG5620 SENSE Arabidopsis thaliana 70 274 73061 CGPG5675 SENSE Rhodopseudomonas palustris 71 275 10180 CGPG57 ANTI-SENSE Arabidopsis thaliana 72 276 73029 CGPG5737 SENSE Saccharomyces cerevisiae 73 277 11145 CGPG574 SENSE Arabidopsis thaliana 74 278 72920 CGPG5763 SENSE Saccharomyces cerevisiae 75 279 72957 CGPG5788 SENSE Saccharomyces cerevisiae 76 280 73044 CGPG5808 SENSE Glycine max 77 281 74323 CGPG5873 SENSE Arabidopsis thaliana 78 282 74327 CGPG5901 SENSE Arabidopsis thaliana 79 283 74329 CGPG5903 SENSE Arabidopsis thaliana 80 284 74340 CGPG5907 SENSE Arabidopsis thaliana 81 285 74341 CGPG5911 SENSE Arabidopsis thaliana 82 286 74345 CGPG5932 SENSE Arabidopsis thaliana 83 287 74616 CGPG6017 SENSE Arabidopsis thaliana 84 288 74604 CGPG6019 SENSE Arabidopsis thaliana 85 289 74608 CGPG6043 SENSE Arabidopsis thaliana 86 290 74609 CGPG6044 SENSE Arabidopsis thaliana 87 291 74366 CGPG6073 SENSE Arabidopsis thaliana 88 292 74383 CGPG6098 SENSE Arabidopsis thaliana 89 293 74374 CGPG6100 SENSE Arabidopsis thaliana 90 294 74618 CGPG6117 SENSE Arabidopsis thaliana 91 295 74619 CGPG6118 SENSE Arabidopsis thaliana 92 296 74622 CGPG6124 SENSE Arabidopsis thaliana 93 297 74628 CGPG6131 SENSE Arabidopsis thaliana 94 298 74631 CGPG6139 SENSE Arabidopsis thaliana 95 299 74669 CGPG6140 SENSE Arabidopsis thaliana 96 300 74670 CGPG6145 SENSE Arabidopsis thaliana 97 301 74647 CGPG6163 SENSE Arabidopsis thaliana 98 302 74385 CGPG6310 SENSE Arabidopsis thaliana 99 303 74386 CGPG6330 SENSE Arabidopsis thaliana 100 304 74387 CGPG6331 SENSE Arabidopsis thaliana 101 305 74685 CGPG6362 SENSE Arabidopsis thaliana 102 306 73487 CGPG6386 SENSE Sinorhizobium meliloti 103 307 73476 CGPG6393 SENSE Bacillus subtilis subsp. subtilis str. 168 104 308 73465 CGPG6400 SENSE Escherichia coli K12 105 309 73418 CGPG6404 SENSE Nostoc punctiforme PCC 73102 106 310 73480 CGPG6425 SENSE Sinorhizobium meliloti 107 311 73482 CGPG6438 SENSE Agrobacterium tumefaciens str. C58 108 312 73513 CGPG6457 SENSE Bacillus subtilis subsp. subtilis str. 168 109 313 73550 CGPG6468 SENSE Bacillus halodurans 110 314 73527 CGPG6474 SENSE Desulfitobacterium hafniense 111 315 73516 CGPG6481 SENSE Xenorhabdus nematophila 112 316 73530 CGPG6498 SENSE Escherichia coli K12 113 317 73534 CGPG6527 SENSE Bacillus subtilis subsp. subtilis str. 168 114 318 74125 CGPG6544 SENSE Pseudomonas fluorescens PfO-1 115 319 74161 CGPG6547 SENSE Escherichia coli K12 116 320 74126 CGPG6552 SENSE Escherichia coli K12 117 321 74115 CGPG6559 SENSE Escherichia coli K12 118 322 74127 CGPG6560 SENSE Escherichia coli K12 119 323 74128 CGPG6568 SENSE Escherichia coli K12 120 324 74165 CGPG6579 SENSE Escherichia coli K12 121 325 74106 CGPG6582 SENSE Pseudomonas fluorescens PfO-1 122 326 74130 CGPG6584 SENSE Pseudomonas syringae pv. tomato str. DC3000 123 327 74132 CGPG6600 SENSE Xenorhabdus nematophila 124 328 74144 CGPG6601 SENSE Xenorhabdus nematophila 125 329 74402 CGPG6663 SENSE Synechocystis sp. 126 330 74476 CGPG6685 SENSE Bacillus halodurans 127 331 74417 CGPG6688 SENSE Bacillus halodurans 128 332 74453 CGPG6691 SENSE Bacillus subtilis subsp. subtilis str. 168 129 333 74418 CGPG6696 SENSE Escherichia coli K12 130 334 10150 CGPG67 ANTI-SENSE Arabidopsis thaliana 131 335 74503 CGPG6767 SENSE Escherichia coli K12 132 336 74504 CGPG6775 SENSE Agrobacterium tumefaciens 133 337 74528 CGPG6777 SENSE Bacillus halodurans 134 338 74588 CGPG6782 SENSE Escherichia coli K12 135 339 74541 CGPG6786 SENSE Escherichia coli K12 136 340 74553 CGPG6787 SENSE Nostoc punctiforme PCC 73102 137 341 74554 CGPG6795 SENSE Pseudomonas syringae pv. tomato str. DC3000 138 342 74578 CGPG6797 SENSE Synechocystis sp. PCC 6803 139 343 74590 CGPG6798 SENSE Xenorhabdus nematophila 140 344 75834 CGPG6820 SENSE Arabidopsis thaliana 141 345 75835 CGPG6822 SENSE Arabidopsis thaliana 142 346 18020 CGPG684 SENSE Arabidopsis thaliana 143 347 75850 CGPG6893 SENSE Arabidopsis thaliana 144 348 75861 CGPG6937 SENSE Arabidopsis thaliana 145 349 75875 CGPG6992 SENSE Arabidopsis thaliana 146 350 74548 CGPG712 SENSE Arabidopsis thaliana 147 351 74880 CGPG7357 SENSE Glycine max 148 352 74903 CGPG7407 SENSE Zea mays 149 353 74915 CGPG7408 SENSE Zea mays 150 354 74927 CGPG7409 SENSE Zea mays 151 355 74951 CGPG7411 SENSE Glycine max 152 356 74940 CGPG7418 SENSE Zea mays 153 357 74977 CGPG7429 SENSE Synechocystis sp. 154 358 74954 CGPG7435 SENSE Xanthomonas campestris 155 359 74907 CGPG7439 SENSE Synechocystis sp. 156 360 74919 CGPG7440 SENSE Synechocystis sp. 157 361 11735 CGPG745 ANTI-SENSE Arabidopsis thaliana 158 362 74980 CGPG7453 SENSE Synechocystis sp. 159 363 74993 CGPG7462 SENSE Bacillus halodurans 160 364 75337 CGPG7469 SENSE Saccharomyces cerevisiae 161 365 75339 CGPG7485 SENSE Zea mays 162 366 75316 CGPG7491 SENSE Glycine max 163 367 75352 CGPG7494 SENSE Zea mays 164 368 12189 CGPG752 ANTI-SENSE Arabidopsis thaliana 165 369 75321 CGPG7531 SENSE Zea mays 166 370 75358 CGPG7542 SENSE Zea mays 167 371 75312 CGPG7554 SENSE Zea mays 168 372 75463 CGPG7583 SENSE Zea mays 169 373 75475 CGPG7584 SENSE Zea mays 170 374 75440 CGPG7589 SENSE Glycine max 171 375 75488 CGPG7593 SENSE Glycine max 172 376 75418 CGPG7603 SENSE Glycine max 173 377 75419 CGPG7611 SENSE Zea mays 174 378 75431 CGPG7612 SENSE Glycine max 175 379 75455 CGPG7614 SENSE Glycine max 176 380 75491 CGPG7617 SENSE Zea mays 177 381 75456 CGPG7622 SENSE Glycine max 178 382 75480 CGPG7624 SENSE Glycine max 179 383 75492 CGPG7625 SENSE Zea mays 180 384 75409 CGPG7626 SENSE Zea mays 181 385 75424 CGPG7651 SENSE Zea mays 182 386 75550 CGPG7676 SENSE Glycine max 183 387 75575 CGPG7686 SENSE Glycine max 184 388 75528 CGPG7690 SENSE Glycine max 185 389 75564 CGPG7693 SENSE Glycine max 186 390 75553 CGPG7700 SENSE Glycine max 187 391 75506 CGPG7704 SENSE Glycine max 188 392 75554 CGPG7708 SENSE Glycine max 189 393 75590 CGPG7711 SENSE Glycine max 190 394 75543 CGPG7715 SENSE Glycine max 191 395 75567 CGPG7717 SENSE Glycine max 192 396 75544 CGPG7723 SENSE Glycine max 193 397 75556 CGPG7724 SENSE Glycine max 194 398 75546 CGPG7739 SENSE Glycine max 195 399 75558 CGPG7740 SENSE Glycine max 196 400 75571 CGPG7749 SENSE Glycine max 197 401 75583 CGPG7750 SENSE Glycine max 198 402 75536 CGPG7754 SENSE Zea mays 199 403 75991 CGPG8266 SENSE Chloroflexus aurantiacus 200 404 75909 CGPG8275 SENSE Chloroflexus aurantiacus 201 405 12824 CGPG885 SENSE Arabidopsis thaliana 202 406 18026 CGPG894 SENSE Arabidopsis thaliana 203 407 11810 CGPG899 ANTI-SENSE Arabidopsis thaliana 204 408 72418 CGPG968 SENSE Arabidopsis thaliana

Recombinant DNA

Exemplary DNA for use in the present invention to improve traits in plants are provided herein as SEQ ID NO:1 through SEQ ID NO:204, as well as the homologs of such DNA molecules. A subset of the exemplary DNA includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of at least 15, preferably at least 16 or 17, more preferably at least 18 or 19, and even more preferably at least 20 or more, consecutive nucleotides. Such oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO:1 through SEQ ID NO:204, and find use, for example as probes and primers for detection of the polynucleotides of the present invention.

Also of interest in the present invention are variants of the DNA provided herein. Such variants may be naturally occurring, including DNA from homologous genes from the same or a different species, or may be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a DNA useful in the present invention may have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.

Homologs of the genes providing DNA of demonstrated as useful in improving traits in model plants disclosed herein will generally demonstrate significant identity with the DNA provided herein. DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; more preferably 70%; more preferably 80% equivalence; more preferably 85% equivalence; more preferably 90%; more preferably 95%; and/or more preferably 98% or 99% equivalence over a comparison window. A comparison window is preferably at least 50-100 nucleotides, and more preferably is the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window may be conducted by algorithms; preferably by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide may be a full-length molecule or a portion of a longer molecule. Preferentially, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.

Proteins useful for imparting improved traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. The term “protein” also includes molecules consisting of one or more polypeptide chains. Thus, a protein useful in the present invention may constitute an entire protein having the desired biological activity, or may constitute a portion of an oligomeric protein having multiple polypeptide chains. Proteins useful for generation of transgenic plants having improved traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 205 through SEQ ID NO: 408, as well as homologs of such proteins.

Homologs of the proteins useful in the present invention may be identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g. manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. As used herein, a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared. An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there may be no ortholog or more than one ortholog. Other complicating factors include alternatively spliced transcripts from the same gene, limited gene identification, redundant copies of the same gene with different sequence lengths or corrected sequence. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. Thus, homolog is used herein to described proteins that are assumed to have functional similarity by inference from sequence base similarity. The relationship of homologs with amino acid sequences of SEQ ID NO:409 to 19247 to the proteins with amino acid sequences of SEQ ID NO:206 to 408 is found in the listing of Table 2.

A further aspect of the invention comprises functional homolog proteins which differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g. valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.

Homologs of the trait-improving proteins disclosed provided herein will generally demonstrate significant sequence identity. Of particular interest are proteins having at least 50% sequence identity, more preferably at least about 70% sequence identity or higher, e.g. at least about 80% sequence identity with an amino acid sequence of SEQ ID NO: 205 through SEQ ID NO: 408. Of course useful proteins also include those with higher identity, e.g. 90% to 99% identity. Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g. the full sequence of any of SEQ ID NO:205 through SEQ ID NO:408.

Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class-(family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g. to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.

In particular embodiments, the inventors contemplate the use of antibodies, either monoclonal or polyclonal which bind to the proteins disclosed herein. Means for preparing and characterizing antibodies are well known in the art (See, e.g., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; incorporated herein by reference). The methods for generating monoclonal antibodies (mAbs) generally begin along the same lines as those for preparing polyclonal antibodies. Briefly, a polyclonal antibody is prepared by immunizing an animal with an immunogenic composition in accordance with the present invention and collecting antisera from that immunized animal. A wide range of animal species can be used for the production of antisera. Typically the animal used for production of anti-antisera is a rabbit, a mouse, a rat, a hamster, a guinea pig or a goat. Because of the relatively large blood volume of rabbits, a rabbit is a preferred choice for production of polyclonal antibodies.

mAbs may be readily prepared through use of well-known techniques, such as those exemplified in U.S. Pat. No. 4,196,265, incorporated herein by reference. Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, e.g., a purified or partially purified antifungal protein, polypeptide or peptide. The immunizing composition is administered in a manner effective to stimulate antibody producing cells. Rodents such as mice and rats are preferred animals, however, the use of rabbit, sheep, or frog cells is also possible. The use of rats may provide certain advantages (Goding, 1986, pp. 60-61), but mice are preferred, with the BALB/c mouse being most preferred as this is most routinely used and generally gives a higher percentage of stable fusions.

Following immunization, somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the mAb generating protocol. The antibody-producing B lymphocytes from the immunized animal are then fused with cells of an immortal myeloma cell, generally one of the same species as the animal that was immunized to establish a population of hybridomas from which specific hybridomas are selected. The selected hybridomas would then be serially diluted and cloned into individual antibody-producing cell lines, which clones can then be propagated indefinitely to provide mAbs.

Promoters

Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens, caulimovirus promoters such as the cauliflower mosaic virus or figwort mosaic virus promoters. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938 which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,378,619 which discloses a Figwort Mosaic Virus (FMV) 35S promoter, U.S. Pat. No. 6,437,217 which discloses a maize RS81 promoter, U.S. Pat. No. 5,641,876 which discloses a rice actin promoter, U.S. Pat. No. 6,426,446 which discloses a maize RS324 promoter, U.S. Pat. No. 6,429,362 which discloses a maize PR-1 promoter, U.S. Pat. No. 6,232,526 which discloses a maize A3 promoter, U.S. Pat. No. 6,177,611 which discloses constitutive maize promoters, U.S. Pat. No. 6,433,252 which discloses a maize L3 oleosin promoter, U.S. Pat. No. 6,429,357 which discloses a rice actin 2 promoter and intron, U.S. Pat. No. 5,837,848 which discloses a root specific promoter, U.S. Pat. No. 6,084,089 which discloses cold inducible promoters, U.S. Pat. No. 6,294,714 which discloses light inducible promoters, U.S. Pat. No. 6,140,078 which discloses salt inducible promoters, U.S. Pat. No. 6,252,138 which discloses pathogen inducible promoters, U.S. Pat. No. 6,175,060 which discloses phosphorus deficiency inducible promoters, U.S. Patent Application Publication 2002/0192813A1 which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors, U.S. patent application Ser. No. 09/078,972 which discloses a coixin promoter, U.S. patent application Ser. No. 09/757,089 which discloses a maize chloroplast aldolase promoter, and U.S. patent application Ser. No. 10/739,565 which discloses water-deficit inducible promoters, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.

Furthermore, the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein may be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted in the forward or reverse orientation 5′ or 3′ to the coding sequence. In some instances, these 5′ enhancing elements are introns. Deemed to be particularly useful as enhancers are the 5′ introns of the rice actin 1 and rice actin 2 genes. Examples of other enhancers that can be used in accordance with the invention include elements from the CaMV 35S promoter, octopine synthase genes, the maize alcohol dehydrogenase gene, the maize shrunken 1 gene and promoters from non-plant eukaryotes.

In some aspects of the invention it is preferred that the promoter element in the DNA construct be capable of causing sufficient expression to result in the production of an effective amount of a polypeptide in water deficit conditions. Such promoters can be identified and isolated from the regulatory region of plant genes that are over expressed in water deficit conditions. Specific water-deficit-inducible promoters for use in this invention are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP17.5), an HVA22 gene (HVA22), a Rab17 gene and a cinnamic acid 4-hydroxylase (CA4H) gene (CA4H) of Zea maize. Such water-deficit-inducible promoters are disclosed in U.S. application Ser. No. 10/739,565, incorporated herein by reference.

In other aspects of the invention, sufficient expression in plant seed tissues is desired to effect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Perl) (Stacy et al. (1996) Plant Mol Biol. 31(6): 1205-1216).

In still other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as SSU (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).

Gene Overexpression

“Gene overexpression” used herein in reference to a polynucleotide or polypeptide indicates that the expression level of a target protein, in a transgenic plant or in a host cell of the transgenic plant, exceeds levels of expression in a non-transgenic plant. In a preferred embodiment of the present invention, a recombinant DNA construct comprises the polynucleotide of interest in the sense orientation relative to the promoter to achieve gene overexpression, which is identified as such in Table 1.

Gene Suppression

Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of integrated recombinant DNA to form double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. This formation of dsRNA most commonly results from transcription of an integrated inverted repeat of the target gene, and is a common feature of gene suppression methods known as anti-sense suppression, co-suppression, RNA interference (RNAi) and knockout, e.g. by mutagenesis. Transcriptional suppression can be mediated by a transcribed dsRNA having homology to a promoter DNA sequence to effect what is called promoter trans suppression.

More particularly, posttranscriptional gene suppression by inserting a recombinant DNA construct with anti-sense oriented DNA to regulate gene expression in plant cells is disclosed in U.S. Pat. No. 5,107,065 (Shewmaker et al.) and U.S. Pat. No. 5,759,829 (Shewmaker et al.). Transgenic plants transformed using such anti-sense oriented DNA constructs for gene suppression can comprise integrated DNA arranged as an inverted repeats that result from insertion of the DNA construct into plants by Agrobacterium-mediated transformation, as disclosed by Redenbaugh et al. in “Safety Assessment of Genetically Engineered Flavr Savr™ Tomato, CRC Press, Inc. (1992). Inverted repeat insertions can comprises a part or all of the T-DNA construct, e.g. an inverted repeat of a complete transcription unit or an inverted repeat of transcription terminator sequence. Screening for inserted DNA comprising inverted repeat elements can improve the efficiency of identifying transformation events effective for gene silencing whether the transformation construct is a simple anti-sense DNA construct which must be inserted in multiple copies or a complex inverted repeat DNA construct (e.g. an RNAi construct) which can be inserted as a single copy.

Posttranscriptional gene suppression by inserting a recombinant DNA construct with sense-oriented DNA to regulate gene expression in plants is disclosed in U.S. Pat. No. 5,283,184 (Jorgensen et al.) and U.S. Pat. No. 5,231,020 (Jorgensen et al.). Inserted T-DNA providing gene suppression in plants transformed with such sense constructs by Agrobacterium is organized predominately in inverted repeat structures, as disclosed by Jorgensen et al., Mol. Gen. Genet., 207:471-477 (1987). See also Stam et al., The Plant Journal, 12(1), 63-82 (1997) who used segregation studies to support Jorgensen's finding that gene silencing is mediated by multimeric transgene T-DNA loci in which the T-DNAs are arranged in inverted repeats. Screening for inserted DNA comprising inverted repeat elements can improve the gene silencing efficiency when transforming with simple sense-orientated DNA constructs. Gene silencing efficiency can also be improved by screening for single insertion events when transforming with an RNAi construct containing inverted repeat elements

As disclosed by Redenbaugh et al. gene suppression can be achieved by inserting into a plant genome recombinant DNA that transcribes dsRNA. Such a DNA insert can be transcribed to an RNA element having the 3′ region as a double stranded RNA. RNAi constructs are also disclosed in EP 0426195 A1 (Goldbach et al. —1991) where recombinant DNA constructs for transcription into hairpin dsRNA for providing transgenic plants with resistance to tobacco spotted wilt virus. Double-stranded RNAs were also disclosed in WO 94/01550 (Agrawal et al.) where anti-sense RNA was stabilized with a self-complementary 3′ segment. Agrawal et al. referred to U.S. Pat. No. 5,107,065 for using such self-stablized anti-sense RNAs for regulating gene expression in plant cells; see International Publication No. 94/01550. Other double-stranded hairpin-forming elements in transcribed RNA are disclosed in International Publication No. 98/05770 (Werner et al.) where the anti-sense RNA is stabilized by hairpin forming repeats of poly(CG) nucleotides. See also U.S. Patent Application Publication No. 2003/0175965 A1 (Lowe et al.) which discloses gene suppression using and RNAi construct comprising a gene coding sequence preceded by inverted repeats of 5′UTR. See also U.S. Patent Application Publication No. 2002/0048814 A1 (Oeller) where RNAi constructs are transcribed to sense or anti-sense RNA which is stabilized by a poly(T)-poly(A) tail. See also U.S. Patent Application Publication No. 2003/0018993 A1 (Gutterson et al.) where sense or anti-sense RNA is stabilized by an inverted repeat of a of the 3′ untranslated region of the NOS gene. See also U.S. Patent Application Publication No. 2003/0036197 A1 (Glassman et al.) where RNA having homology to a target is stabilized by two complementary RNA regions.

Gene silencing can also be effected by transcribing RNA from both a sense and an anti-sense oriented DNA, e.g. as disclosed by Shewmaker et al. in U.S. Pat. No. 5,107,065 where in Example 1a binary vector was prepared with both sense and anti-sense aroA genes. See also U.S. Pat. No. 6,326,193 where gene targeted DNA is operably linked to opposing promoters.

Gene silencing can also be affected by transcribing from contiguous sense and anti-sense DNA. In this regard see Sijen et al., The Plant Cell, Vol. 8, 2277-2294 (1996) discloses the use of constructs carrying inverted repeats of a cowpea mosaic virus gene in transgenic plants to mediate virus resistance. Such constructs for posttranscriptional gene suppression in plants by double-stranded RNA are also disclosed in International Publication No. WO 99/53050(Waterhouse et al.), International Publication No. WO 99/49029 (Graham et al.), U.S. patent application Ser. No. 10/465,800 (Fillatti), U.S. Pat. No. 6,506,559 (Fire et al.). See also U.S. application Ser. No. 10/393,347 (Shewmaker et al.) that discloses constructs and methods for simultaneously expressing one or more recombinant genes while simultaneously suppressing one or more native genes in a transgenic plant. See also U.S. Pat. No. 6,448,473 (Mitsky et al.) that discloses multi-gene suppression vectors for use in plants. All of the above-described patents, applications and international publications disclosing materials and methods for posttranscriptional gene suppression in plants are incorporated herein by reference. Transcriptional suppression such as promoter trans suppression can be affected by a expressing a DNA construct comprising a promoter operably linked to inverted repeats of promoter DNA for a target gene. Constructs useful for such gene suppression mediated by promoter trans suppression are disclosed by Mette et al., The EMBO Journal, Vol. 18, No. 1, pp. 241-148, 1999 and by Mette et al., The EMBO Journal, Vol. 19, No. 19, pp. 5194-5201-148, 2000, both of which are incorporated herein by reference.

Suppression can also be achieved by insertion mutations created by transposable elements may also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium may be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants may be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.

Gene Stacking

The present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with a multiple desired traits. The combinations generated can include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.

Plant Cell Transformation Methods

Numerous methods for transforming plant cells with recombinant DNA are known in the art and may be used in the present invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. Nos. 5,015,580 (soybean); 5,550,318 (corn); 5,538,880 (corn); 5,914,451 (soybean); 6,160,208 (corn); 6,399,861 (corn) and 6,153,812 (wheat) and Agrobacterium-mediated transformation is described in U.S. Pat. Nos. 5,159,135 (cotton); 5,824,877 (soybean); 5,591,616 (corn); and 6,384,301 (soybean), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation system, additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.

In general it is useful to introduce recombinant DNA randomly, i.e. at a non-specific location, in the genome of a target plant line. In special cases it may be useful to target recombinant DNA insertion in order to achieve site-specific integration, for example to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function implants include cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.

Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment. “Media” refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism. Recipient cell targets include, but are not limited to, meristem cells, callus, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation. Practical transformation methods and materials for making transgenic plants of this invention, for example various media and recipient target cells, transformation of immature embryo cells and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526, which are incorporated herein by reference.

The seeds of transgenic plants can be harvested from fertile transgenic plants and be used to grow progeny generations of transformed plants of this invention including hybrid plants line for selection of plants having an enhanced trait. In addition to direct transformation of a plant with a recombinant DNA, transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA. For example, recombinant DNA can be introduced into first plant line that is amenable to transformation to produce a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line

In the practice of transformation DNA is typically introduced into only a small percentage of target plant cells in any one transformation experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a transgenic DNA construct into their genomes. Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers. Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA. Commonly used selective marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (nptII), hygromycin B (aph IV) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat) and glyphosate (aroA or EPSPS). Examples of such selectable are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.

Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, may be cultured in regeneration media and allowed to mature into plants. Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO₂, and 25-250 microeinsteins m⁻² s⁻¹ of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue. Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn. The regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.

Transgenic Plants and Seeds

Transgenic plants derived from the plant cells of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention. Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.

Discovery of Trait-Improving Recombinant DNA

To identify recombinant DNA that imparts an enhanced trait to plants, Arabidopsis cells were transformed with a candidate recombinant DNA construct and screened for an improved trait. A two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more improved traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an improved trait. The following Table 3 summarizes the improved traits that have been confirmed as provided by a recombinant DNA construct.

In particular, Table 3 reports

“PEP SEQ ID” which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing. “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit. The components of “annotation” are “e-value” which provides the expectation value for the BLAST hit; “% id” which refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank; “GenBank ID” which provides a reference number for the top BLAST hit in GenBank; and “description” which refers to the description of that top BLAST hit. “traits” identify by two letter codes the confirmed improvement in a transgenic plant provided by the recombinant DNA. The codes for improved traits are: “CK” which indicates cold tolerance improvement identified under a cold shock tolerance screen; “CS” which indicates cold tolerance improvement identified by a cold germination tolerance screen; “DS” which indicates drought tolerance improvement identified by a soil drought stress tolerance screen; “PEG” which indicates osmotic stress tolerance improvement identified by a PEG induced osmotic stress tolerance screen; “HS” which indicates heat stress tolerance improvement identified by a heat stress tolerance screen; “SS” which indicates high salinity stress tolerance improvement identified by a salt stress tolerance screen; “LN” which indicates nitrogen use efficiency improvement identified by a limited nitrogen tolerance screen; “LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition; “PP” which indicates improved growth and development at early stages identified by an early plant growth and development screen; “SP” which indicates improved growth and development at late stages identified by a late plant growth and development screen provided herein.

TABLE 3 PEP annotation SEQ e- % ID value id GenBank ID description Traits 205 5.00E−34 85 gi|21281159| gb|AAD48981.1|contains HS similarity to Solanum lycopersicum (tomato) wound induced protein 206 1.00E−66 76 gi|21553397| gb|AAM62490.1|putative zinc LN finger protein 207 1.00E−118 93 gi|7573441| ref|NP_191871.1|cyclin HS family protein 208 0 93 gi|22136838| ref|NP_566299.1|GPI CK CS transamidase component Gpi16 subunit family protein 209 1.00E−171 97 gi|15028251| ref|NP_566244.1| CK transmembrane protein, putative 210 2.00E−57 98 gi|37202020| emb|CAB81279.1|putative HS PP PEG protein 211 8.00E−37 100 gi|26451972| dbj|BAC43077.1|unknown PP SS HS protein 212 0 86 gi|42562765| ref|NP_175971.3|transcription CK factor-related 213 0 100 gi|21280989| gb|AAM44902.1|putative PP SP catalase 214 0 89 gi|22087278| gb|AAC97995.1|Similar to LN PP HS gb|Z30094 basic transcripion factor 2, 44 kD subunit from Homo sapiens. 215 0 77 gi|12324313| gb|AAD55662.1|Highly similar DS to non intermediate filament IFA binding protein 216 0 100 gi|21537362| gb|AAM61703.1|protein CK kinase-like protein 217 0 87 gi|4678332| emb|CAB41143.1|putative CK peptide transporter 218 1.00E−144 86 gi|14532890| gb|AAK64127.1|unknown PEG protein 219 1.00E−145 95 gi|3242721| gb|AAC23773.1|putative DS acetone-cyanohydrin lyase 220 0 84 gi|15293165| gb|AAK93693.1|putative 3- CK PEG CS HS PP methyladenine DNA glycosylase 221 1.00E−178 79 gi|6321581| ref|NP_011658.1|Btn2p PP [Saccharomyces cerevisiae] 222 0 98 gi|30387605| ref|NP_178499.2|MATE LN efflux family protein 223 1.00E−147 90 gi|9758099| ref|NP_198887.1|zinc finger CS (C2H2 type) family protein 224 1.00E−139 95 gi|23505833| gb|AAN28776.1|At3g51780/ORF3 CK 225 0 100 gi|6729028| gb|AAF27024.1|putative CS nodulin [Arabidopsis thaliana] ref|NP_187169.1|GDSL-motif lipase/hydrolase family protein 226 0 100 gi|21436143| gb|AAM51318.1|unknown CS protein 227 0 97 gi|31711910| gb|AAM64944.1|betaine PP aldehyde dehydrogenase, putative 228 1.00E−128 80 gi|21554268| ref|NP_171616.1|33 kDa PEG SS ribonucleoprotein, chloroplast, putative/RNA-binding protein cp33, putative 229 0 95 gi|6321563| emb|CAA58159.1|glutamic- CK CS SS dependent asparagine synthase 230 1.00E−132 57 gi|25403213| pir||A86468probable zinc PP PEG finger protein 231 2.00E−54 52 gi|20127115| gb|AAM10965.1|putative CK bHLH transcription factor [Arabidopsis thaliana] 232 1.00E−160 72 gi|18401370| ref|NP_566566.1|protein CK HS PEG CS phosphatase 2C family protein 233 1.00E−33 45 gi|21593875| gb|AAM65842.1|putative PP HS RING-H2 zinc finger protein 234 2.00E−34 51 gi|55419648| gb|AAV51937.1|AP2/EREBP CK transcription factor ERF-2 235 2.00E−73 59 gi|3955021| emb|CAA09367.1|HB2 CK CS homeodomain protein 236 1.00E−51 58 gi|4689366| gb|AAD27870.1|BRH1 RING HS PP PEG finger protein 237 1.00E−149 76 gi|52354283| gb|AAM14913.1|putative HS malonyl-CoA:Acyl carrier protein transacylase 238 1.00E−154 85 gi|20260680| gb|AAM13238.1|putative PP PEG NADPH-dependent mannose 6-phosphate reductase 239 2.00E−89 64 gi|21593394| ref|NP_567300.1|short-chain HS dehydrogenase/reductase (SDR) family protein 240 0 82 gi|42795470| gb|AAS46245.1|HMG-CoA CK HS SS synthase 2 241 1.00E−113 83 gi|20385588| gb|AAM21344.1|MADS-box SP protein 4 242 1.00E−135 89 gi|21280889| ref|NP_196254.1|ribosomal SS HS protein S8e family protein 243 5.00E−28 43 gi|4567308| gb|AAD23719.1|putative PEG RING zinc finger protein 244 3.00E−35 33 gi|25352200| pir||T52379zinc finger protein PEG ZPT3-3 245 0 83 gi|10800918| emb|CAC12995.1|putative CK PEG CS AUX1-like permease 246 3.00E−61 87 gi|21554008| gb|AAM63089.1|cold- CS HS PP regulated protein cor15b precursor 247 0 100 gi|25406415| pir||D96781cytochrome P450, PEG probable, 64213-66051 248 0 92 gi|3885330| gb|AAC77858.1|putative PP cytochrome P450 249 1.00E−159 100 gi|21593400| gb|AAM65367.1|phi-1-like LN LL protein 250 1.00E−89 76 gi|45825151| ref|NP_200258.2|zinc finger DS (B-box type) family protein 251 1.00E−144 72 gi|3643085| gb|AAC36698.1|protein PP CK phosphatase-2C; PP2C 252 2.00E−90 91 gi|21537084| gb|AAM61425.1|unknown CK PEG 253 2.00E−51 100 gi|28393947| ref|NP_174092.1|glycine-rich HS PP protein 254 0 91 gi|23197704| ref|NP_565909.1|radical SAM PEG domain-containing protein 255 0 93 gi|4902476| emb|CAB43520.1|MAP kinase CK CS 256 1.00E−100 72 gi|34146806| gb|AAC34217.1|putative CS alcohol dehydrogenase 257 2.00E−87 82 gi|3548814| gb|AAC34486.1|E3 ubiquitin CK LL CS ligase SCF complex subunit SKP1/ASK1 (At19), 258 1.00E−113 81 gi|7939553| dbj|BAA95756.1|expansin-like PP HS protein 259 1.00E−163 52 gi|13506810| gb|AAK28345.1|receptor-like CK PP protein kinase 3 260 1.00E−163 68 gi|12597803| gb|AAG60115.1|hypothetical PP protein 261 1.00E−161 100 gi|20258881| gb|AAM14112.1|putative LL ubiquinone/menaquinone biosynthesis methyltransferase 262 1.00E−133 92 gi|12597757| ref|NP_176849.1|nodulin SS PEG MtN3 family protein 263 0 95 gi|6911875| sp|P53780|METC_ARATH PP SS Cystathionine beta-lyase, chloroplast precursor (CBL) (Beta-cystathionase) (Cysteine lyase) 264 1.00E−100 100 gi|21389647| gb|AAM48022.1|photoassimilate- SP DS responsive protein PAR-1b- like protein 265 0 100 gi|25402889| ref|NP_173376.1|very-long- PEG PP chain fatty acid condensing enzyme, putative 266 0 88 gi|6324999| sp|P20438|CG12_YEAST DS G1/S-specific cyclin CLN2 gb|AAA65725.1|cyclin 2 267 0 100 gi|3218550| dbj|BAA28775.1|Cdk- LL activating kinase 1At 268 1.00E−169 100 gi|6321880| ref|NP_011956.1|Nucleolar SP protein involved in the assembly of the large ribosomal subunit; contains a sigma(70)-like motif, which is thought to bind RNA 269 0 89 gi|21436315| gb|AAM51327.1|putative CK HS CS histidyl-tRNA synthetase 270 1.00E−150 100 gi|14318575| ref|NP_116708.1|20S PP PEG SS proteasome beta-type subunit 271 0 99 gi|6325396| pir||S69027 ammonium LL DS transport protein MEP3 272 5.00E−76 72 gi|7442240| sp|O24543|AX2E_PHAAU DS Auxin-induced protein 22E (Indole-3-acetic acid induced protein ARG14) 273 0 94 gi|9759247| dbj|BAB09771.1|serine/threonine LL protein kinase-like protein 274 0 97 gi|39647867| emb|CAE26387.1|phosphogly CK DS CS cerate kinase 275 0 89 gi|9758468| dbj|BAB08997.1|monosaccharide PP PEG transporter 276 1.00E−66 80 gi|6319966| ref|NP_010046.1|Phosphorelay HS intermediate protein, phosphorylated by the plasma membrane sensor Sln1p in response to osmotic stress and then in turn phosphorylates the response regulators Ssk1p in the cytosol and Skn7p in the nucleus 277 2.00E−88 83 gi|21536637| ref|NP_565524.1|stress DS LN enhanced protein 2 (SEP2) 278 0 90 gi|6322724| ref|NP_012797.1|Required for SS transcription of rDNA by RNA Polymerase I; DNA- independent RNA Polymerase I transcription factor 279 0 94 gi|6320705| pir||S69555 myo-inositol HS SS PP transport protein ITR1 - yeast) 280 5.00E−24 49 gi|25453551| pir||T52011ethylene LL responsive element binding factor 3 281 1.00E−150 100 gi|4580468| gb|AAD24392.1|putative PP cAMP-dependent protein kinase 282 1.00E−169 91 gi|21436057| ref|NP_193037.1| LL SS oxidoreductase, zinc-binding dehydrogenase family protein 283 1.00E−165 83 gi|21280925| gb|AAM44967.1|putative HS cinnamyl alcohol dehydrogenase 284 0 100 gi|20334800| ref|NP_568453.1|alcohol PEG dehydrogenase, putative [Arabidopsis thaliana] 285 0 100 gi|22136298| gb|AAM91227.1|alcohol PP dehydrogenase 286 1.00E−144 89 gi|20259173| sp|O04202|IF35_ARATH CS SS CK Eukaryotic translation initiation factor 3 subunit 5 (eIF-3 epsilon) (eIF3 p32 subunit) (eIF3f) 287 6.00E−74 96 gi|21593170| ref|NP_196239.1|RNA- PP binding protein, putative 288 1.00E−112 80 gi|9759521| dbj|BAB10987.1|nuclear cap- PP binding protein; CBP20 289 1.00E−177 95 gi|12083276| gb|AAG48797.1|putative delta CS PEG 9 desaturase 290 1.00E−111 94 gi|12083264| gb|AAG48791.1|putative GTP- LN SS PP binding protein RAB11D 291 1.00E−134 91 gi|23505935| gb|AAP86673.1|26S HS SS proteasome subunit RPN12 292 3.00E−53 86 gi|26452894| dbj|BAC43525.1|putative CK HS PP SS PEG CS DNA-directed RNA polymerase 14 kDa subunit AtRPAC14 293 5.00E−94 100 gi|21554412| gb|AAM63517.1|probable CK CS PEG PP glutathione peroxidase At2g31570 294 1.00E−116 92 gi|6143884| ref|NP_187617.1| SP CK immunophilin, putative/ FKBP-type peptidyl-prolyl cis- trans isomerase, putative 295 1.00E−114 100 gi|6671929| gb|AAF23189.1|putative GTP- PP binding protein (ATFP8) [Arabidopsis thaliana] 296 1.00E−161 92 gi|7670024| ref|NP_566563.1|ubiquitin- HS PP SS conjugating enzyme, putative 297 1.00E−132 95 gi|21554045| gb|AAM63126.1|20S SS proteasome subunit PAC1 298 1.00E−111 94 gi|21593047| gb|AAM64996.1|GTP-binding PP protein Rab11 299 0 93 gi|23308437| ref|NP_190336.1|malate SS HS dehydrogenase [NAD], chloroplast (MDH) 300 3.00E−94 80 gi|6562282| emb|CAB62652.1|rac-like PEG GTP binding protein Arac11 301 0 100 gi|21554607| gb|AAM63631.1|ubiquitin SS activating enzyme-like protein 302 5.00E−26 81 gi|15217910| ref|NP_173453.1|homeobox- PP leucine zipper protein-related 303 1.00E−129 86 gi|23505995| ref|NP_177122.2|acid SP PP phosphatase, putative [Arabidopsis thaliana] 304 1.00E−157 100 gi|28827628| gb|AAO50658.1|putative C-4 PP sterol methyloxidase 305 9.00E−19 100 gi|21592539| ref|NP_565794.1| CS SS CK hydroxyproline-rich glycoprotein family protein [Arabidopsis thaliana] 306 0 97 gi|15965196| ref|NP_385549.1|PROBABLE SP LL ENOLASE PROTEIN 307 1.00E−153 100 gi|16080137| pir||A69990 UTP-glucose-1- LL phosphate uridylyltransferase homolog ytdA 308 1.00E−147 98 gi|26246388| ref|NP_752427.1|Pyrroline-5- LN carboxylate reductase 309 1.00E−135 94 gi|23126946| ref|ZP_00108826.1|COG0345: PP Pyrroline-5-carboxylate reductase 310 0 100 gi|16263079| ref|NP_435872.1|probable PEG alcohol 311 0 99 gi|15888903| pir||H97551 probable LL aminotransferase aatc 312 0 90 gi|16080158| ref|NP_390984.1|glycine CS CK betaine aldehyde dehydrogenase 313 1.00E−141 94 gi|15614866| ref|NP_243169.1|UTP- PP glucose-1-phosphate uridylyltransferas 314 0 99 gi|23111329| ref|ZP_00097007.1|COG0205: CS PP CK 6-phosphofructokinase 315 1.00E−150 87 gi|37526393| ref|NP_929737.1|UTP-- PEG SS glucose-1-phosphate uridylyltransferase (UDP- glucose pyrophosphorylase) (UDPGP) 316 0 99 gi|16128895| ref|NP_415448.1|aspartate PP aminotransferase 317 0 97 gi|16080149| ref|NP_390975.1|glucose-1- DS phosphate adenylyltransferase 318 0 96 gi|48732455| ref|ZP_00266198.1|COG1012: HS PP NAD-dependent aldehyde dehydrogenases 319 0 97 gi|16129263| ref|NP_415818.1|4- SS PP aminobutyrate aminotransferase 320 0 99 gi|16128583| ref|NP_415133.1|putative PP PLP-dependent aminotransferase 321 0 99 gi|30063716| ref|NP_837887.1|putative CS CK aminotransferase 322 0 99 gi|16130084| ref|NP_416651.1|bifunctional: SS PP putative glutamate synthase (N-terminal); putative oxidoreductase (C-terminal) 323 0 94 gi|16128664| ref|NP_415214.1|phosphoglucomutase SP PP 324 0 96 gi|49176307| ref|NP_417544.3|probable CS CK ornithine aminotransferase [Escherichia coli K12] (EC 2.6.1.13) 325 1.00E−175 80 gi|48729503| ref|ZP_00263253.1|COG0508: CK PP Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes 326 1.00E−173 80 gi|28869402| ref|NP_792021.1|2- CK PP oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase 327 1.00E−161 90 gi|37524574| ref|NP_927918.1|Transaldolase B PP 328 0 82 gi|37525385| ref|NP_928729.1|Dihydrolipoamide LN PP succinyltransferase component of 2-oxoglutarate dehydrogenase complex (E2) 329 3.00E−55 86 gi|16332334| ref|NP_443062.1|hypothetical CS PP HS protein slr0607 330 0 100 gi|15614388| ref|NP_242691.1|acetoin LL dehydrogenase E3 component 331 0 99 gi|15615327| ref|NP_243630.1|dihydrolipoamide LN dehydrogenase 332 0 97 gi|16078525| ref|NP_389344.1|dihydrolipoamide HS DS dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2- oxoglutarate dehydrogenase complexes 333 0 94 gi|15800431| ref|NP_286443.1|2- CS CK oxoglutarate dehydrogenase 334 0 89 gi|22136798| gb|AAM91743.1|putative LN phosphate/phosphoenolpyruvate translocator precursor protein 335 0 100 gi|49176098| ref|NP_415825.3|putative HS SS polysaccharide hydrolase 336 0 96 gi|15889444| ref|NP_355125.1|AGR_C_3927p CK HS PP PEG CS SS [Agrobacterium tumefaciens str. C58] ref|NP_532838.1| bacteriophytochrome protein 337 0 95 gi|15613173| ref|NP_241476.1|sulfite PP CK CS PEG reductase (NADPH) 338 0 100 gi|30062749| ref|NP_836920.1|nitrate LN reductase 1, beta subunit 339 0 100 gi|15804618| ref|NP_290659.1|glucosephosphate PP CS isomerase 340 0 100 gi|23125493| ref|ZP_00107424.1|COG0243: PP PEG HS Anaerobic dehydrogenases, typically selenocysteine- containing 341 0 98 gi|28868179| ref|NP_790798.1|glucose-6- CK PP SP PEG CS phosphate isomerase 342 0 96 gi|16329427| ref|NP_440155.1|isocitrate CK CS dehydrogenase (NADP+) 343 0 85 gi|37524705| ref|NP_928049.1|sulfite DS PP PEG reductase [NADPH] hemoprotein beta-component (SIR-HP) 344 1.00E−121 95 gi|6728966| gb|AAF26964.1|unknown LN protein 345 0 96 gi|6714417| gb|AAF26105.1|unknown LN protein 346 0 78 gi|22136866| ref|NP_177343.2|protease- CS associated zinc finger (C3HC4-type RING finger) family protein 347 0 92 gi|51971567| ref|NP_850943.1|glutamine CK HS CS amidotransferase-related 348 2.00E−65 88 gi|26450572| dbj|BAC42398.1|unknown CK CS protein [Arabidopsis thaliana] 349 1.00E−115 100 gi|6730712| gb|AAF27107.1|Unknown CK CS protein 350 0 100 gi|20465757| gb|AAM20367.1|putative PP cyclin protein 351 8.00E−90 56 gi|23297314| ref|NP_849559.1|WRKY CK CS family transcription factor [Arabidopsis thaliana] 352 1.00E−171 83 gi|50940357| ref|XP_479706.1|putative PP HS SS Shwachman-Bodian-Diamond syndrome protein 353 2.00E−46 92 gi|50929801| ref|XP_474428.1|OSJNBa007 CK PP 0M12.6 354 7.00E−54 92 gi|5042333| emb|CAB44664.1|BETL4 PP protein 355 1.00E−56 34 gi|42563228| ref|NP_565108.2|zinc finger HS SS PEG (CCCH-type) family protein 356 4.00E−61 72 gi|51970440| dbj|BAD43912.1|hypothetical CK PP protein 357 7.00E−91 99 gi|16331395| ref|NP_442123.1|hypothetical SS protein slr0013 358 0 99 gi|21229841| ref|NP_635758.1|vanillate O- CS CK demethylase oxygenase subunit 359 1.00E−142 100 gi|16331855| sp|Q55891|PCYA_SYNY3 CK PP CS Phycocyanobilin: ferredoxin oxidoreductase 360 0 100 gi|16331872| ref|NP_442600.1|hypothetical SP CK protein slr0304 361 3.00E−86 87 gi|21593344| gb|AAM65293.1|putative cold- LN regulated protein ref|NP_178469.1|late embryogenesis abundant domain-containing protein/ LEA domain-containing protein 362 8.00E−91 100 gi|16330328| sp|P73690|Y51L_SYNY3 HS Ycf51-like protein dbj|BAA17736.1| ORF_ID: sll1702~hypothetical protein 363 5.00E−87 100 gi|15612647| ref|NP_240950.1|hypoxanthine- PEG SS guanine phosphoribosyltransferase 364 0 83 gi|6323679| sp|P23748|MPIP_YEAST M- CS LL PP CK HS SS phase inducer phosphatase (Mitosis initiation protein MIH1) (Mitotic inducer homolog) 365 2.00E−33 90 gi|34898476| ref|NP_910584.1|EST PP AU082567(S21715) corresponds to a region of the predicted gene.~Similar to S. tuberosum ubiquinol cytochrome c reductase. (X79275) 366 6.00E−54 81 gi|21592528| gb|AAM64477.1|ring-box HS SS protein-like 367 0 76 gi|34910110| dbj|BAB92553.1|DNA cross- CK HS link repair 1B-like protein 368 1.00E−156 100 gi|21436267| gb|AAM51272.1|putative LN nodulin-26 protein 369 1.00E−100 81 gi|50900588| ref|XP_462727.1|putative LN phenylalkylamine binding protein sp|Q9FTZ2|EBP_ORYSA Probable 3-beta- hydroxysteroid- delta(8),delta(7)-isomerase (Cholestenol delta-isomerase) (Delta8-delta7 sterol isomerase) (D8-D7 sterol isomerase) dbj|BAB92148.1| putative C-8,7 sterol isomerase 370 4.00E−39 46 gi|25361093| pir||T00967hypothetical HS protein At2g26340 371 2.00E−78 89 gi|50906887| ref|XP_464932.1|cytochrome LL PP c biogenesis protein-like 372 1.00E−22 98 gi|50899510| ref|XP_450543.1|unknown CK LL CS PP SS protein 373 5.00E−79 85 gi|50934647| ref|XP_476851.1|bifunctional CK CS phosphopantetheine adenylyl transferase dephospho CoA kinase-like protein 374 8.00E−56 50 gi|38257027| dbj|BAD01556.1|ERF-like PP protein 375 1.00E−64 55 gi|18423944| ref|NP_568850.1|basic helix- PP loop-helix (bHLH) family protein 376 1.00E−39 42 gi|42567912| ref|NP_568344.2|myb family SP PEG transcription factor 377 6.00E−89 84 gi|37535020| ref|NP_921812.1|putative LN HAM-1-like protein 378 2.00E−49 59 gi|27804371| gb|AAO22987.1|MADS-box LL SS transcription factor CDM104 379 2.00E−68 60 gi|22137112| emb|CAB72174.1|responce CK SS reactor 4 [Arabidopsis thaliana] 380 0 89 gi|50910245| ref|XP_466611.1|putative CS CK PLRR-4 polymorphic leucine- rich repeat protein 381 2.00E−30 44 gi|17933450| gb|AAK70215.1|MADS-box CS CK PEG protein 382 1.00E−93 54 gi|20502508| dbj|BAB91414.1|E2F-like CK PEG CS repressor E2L3 383 2.00E−38 58 gi|50909627| ref|XP_466302.1|unknown PEG protein 384 3.00E−41 63 gi|50399946| gb|AAT76334.1|putative DNA- HS directed RNA polymerase II subunit 385 4.00E−59 68 gi|37535924| ref|NP_922264.1|unknown LN protein 386 8.00E−57 58 gi|50944571| ref|XP_481813.1|transfactor- HS like 387 3.00E−73 42 gi|53792319| dbj|BAD53026.1|putative ring LN finger protein 1 388 9.00E−93 47 gi|25054862| ref|NP_850517.1| LN transcription factor, putative/ zinc finger (C3HC4 type RING finger) family protein 389 7.00E−91 66 gi|20269059| emb|CAC84710.1|aux/IAA PEG protein 390 2.00E−72 45 gi|26450026| ref|NP_172358.1|myb family LL LN transcription factor (MYB60) 391 1.00E−80 46 gi|50946213| ref|XP_482634.1|AP2/EREBP LN transcription factor-like protein 392 8.00E−54 43 gi|29824137| ref|NP_189337.1|TCP family CK CS transcription factor, putative [Arabidopsis thaliana] 393 0 99 gi|558543| emb|CAA85320.1|C-terminal HS PP PEG zinc-finger 394 1.00E−124 62 gi|20259301| ref|NP_566010.1|SET PP SS domain-containing protein (ASHH3) 395 4.00E−54 65 gi|21553740| gb|AAM62833.1|putative zinc PP PEG CS finger protein 396 2.00E−54 40 gi|20465561| ref|NP_974448.1|zinc finger LL LN (C3HC4-type RING finger) family protein 397 1.00E−112 65 gi|51557078| gb|AAU06309.1|MYB PP LN transcription factor 398 0 82 gi|15148926| gb|AAK84890.1|TGA-type LN basic leucine zipper protein TGA2.2 399 6.00E−78 47 gi|28558782| gb|AAO45753.1|RING/C3HC4/ LN PHD zinc finger-like protein 400 0 67 gi|42565068| ref|NP_188743.3|transducin HS family protein/WD-40 repeat family protein 401 7.00E−29 46 gi|38638682| ref|NP_177307.1|AP2 CS LL LN domain-containing transcription factor, putative 402 0 84 gi|50904461| ref|XP_463719.1|P0466H10.27 PEG 403 0 88 gi|53796982| ref|ZP_00357872.1|COG0160: SP CS 4-aminobutyrate aminotransferase and related aminotransferases 404 0 94 gi|53796007| ref|ZP_00357032.1|COG0696: PP SS PEG HS Phosphoglyceromutase 405 0 93 gi|30697938| ref|NP_201207.2|expressed DS HS protein 406 0 100 gi|13878095| gb|AAK44125.1|unknown DS CS protein 407 0 97 gi|12324320| gb|AAG52129.1|hypothetical LL protein; 63994-65574 408 0 84 gi|22136086| gb|AAM91121.1|photoreceptor- CS PP interacting protein-like

Trait Improvement Screens

DS-Improvement of drought tolerance identified by a soil drought stress tolerance screen: Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA may find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.

PEG-Improvement of drought tolerance identified by PEG induced osmotic stress tolerance screen: Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits et al. (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.

SS-Improvement of drought tolerance identified by high salinity stress tolerance screen: Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, (3) toxic effects caused by the salt ions, e.g. inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants to maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with improved drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.

HS-Improvement of drought tolerance identified by heat stress tolerance screen: Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes may also impart improved drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.

CK and CS-Improvement of tolerance to cold stress: Low temperature may immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, i.e. cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating. The trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.

Improvement of tolerance to multiple stresses: Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, i.e. multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, PEP SEQ ID NO: 229 and PEP SEQ ID NO: 372 can be used to improve both salt stress tolerance and cold stress tolerance in plants. Of particular interest, plants transformed with PEP SEQ ID NO: 364 can resist heat stress, salt stress and cold stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.

PP-Improvement of early plant growth and development: It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems, that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants may also be used to generate transgenic plants that are more resistant to various stress conditions due to improved early plant development. The present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g. PEP SEQ ID NO: 372 which can improve the plant early growth and development, and impart salt and cold tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.

SP-Improvement of late plant growth and development: “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have improved development during leaf development and seed maturation providing a higher yield potential as compared to control plants.

LL-Improvement of tolerance to shade stress identified in a low light screen: The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by the present invention may be suitable for a higher density planting, thereby resulting increased yield per unit area.

LN-Improvement of Tolerance to Low Nitrogen Availability Stress

Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.

According to the present invention, transgenic plants generated using the recombinant nucleotides, which confer enhanced nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, increased number of green leaves, increased number of rosette leaves, increased root length and advanced flower bud formation. One skilled in the art may recognize that the transgenic plants provided by the present invention with enhanced nitrogen use efficiency may also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention may be productively cultivated under nitrogen nutrient deficient conditions, i.e. nitrogen-poor soils and low nitrogen fertilizer inputs, that would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also may be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.

Stacked Traits: The present invention also encompasses transgenic plants with stacked engineered traits, e.g. a crop having an improved phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.

Once one recombinant DNA has been identified as conferring an improved trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g. bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 204, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 205 to through SEQ ID NO: 408. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 205 through SEQ ID NO: 408. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.

The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with improved traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention may be of any plant species, i.e., may be monocotyledonous or dicotyledonous. Preferably, they will be agricultural useful plants, i.e., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention. Other plants of interest in the present invention for production of transgenic plants having improved traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.

In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly improved traits as the transgenic Arabidopsis counterpart. Improved physiological properties in transgenic plants of the present invention may be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect improved responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures may be made on greenhouse or field grown plants and may include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.

Trait data on morphological changes may be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits may be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain may be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.

To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it may be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g. in Iowa, Ill. or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g. under drought or population density stress.

Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.

The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.

EXAMPLE 1

This example illustrates the identification of recombinant DNA that confers improved trait(s) to plants

A large set of genes of interest were cloned from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter. The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold et al. Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed. The plants and seeds were screened for an enhanced trait or a surrogate for an enhanced trait.

Soil Drought Tolerance Screen

This screen identified genes for recombinant DNA that imparts enhanced water use efficiency as shown in Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions

T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company. USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m²/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.

To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.

At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.

Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). Table 4 provides a list of recombinant DNA constructs that improve drought tolerance in transgenic plants.

TABLE 4 Wilt Response Seed Survival Anaysis of Risk score Weight/plant wilt response Pep RS p- p- diff time p- SEQ ID Construct_id Orientation mean value c delta value c to wilting value c 215 19116 ANTI-SENSE 0 0.795 S −0.341 0.795 / 0.52 0.077 T 250 70677 SENSE 0.045 0.982 S −5.73 0.982 / 0.14 0.07 T 219 72712 SENSE 0.002 0.986 S −2.822 0.986 / 0.64 0.242 / 266 72714 SENSE 0.01 0 S 1.253 0 S 0.14 0.059 T 271 72721 SENSE 0.05 0.834 T −0.129 0.834 / 0 1 / 272 72959 SENSE 0.001 0.172 S 0.341 0.172 / 0.42 0.32 / 317 73534 SENSE 0.006 0.732 S −0.195 0.732 / −0.14 0.724 / 264 74244 SENSE 0.012 0.984 S −0.512 0.984 / 0.13 0.54 / 332 74453 SENSE 0.655 0.001 / 0.886 0.001 S −0.15 0.468 / S: represents that the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05, p value, of the delta of a quantitative response or of the risk score of a qualitative response, is the probability that the observed difference between the transgenic plants and the reference occur by chance) T: represents that the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.

Heat Stress Tolerance Screen

Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This screen identified genes for recombinant DNA that imparts enhanced heat tolerance as shown in Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.

T2 seeds were plated on ½×MS salts, 1/% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m²/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes et al. (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. Table 5 provides a list of recombinant DNA constructs that improve heat tolerance in transgenic plants.

TABLE 5 seedling weight Root Length growth stage Pep p- p- RS p- SEQ ID Construct_id Orientation delta value c delta value c mean value c 258 10903 ANTI-SENSE 1.26 0 S 0.131 0.053 T 0.86 0.051 T 205 12360 SENSE 1.305 0 S 0.142 0.052 T 0.307 0.043 S 405 12824 SENSE 1.309 0 S 0.25 0.002 S 0.63 0.063 T 211 12927 SENSE 1.527 0 S 0.268 0.013 S 0.803 0.018 S 207 15210 SENSE 1.189 0 S 0.121 0.029 S 0.636 0.079 T 214 17309 SENSE 1.29 0 S 0.176 0.01 S 0.581 0.044 S 242 19801 SENSE 1.156 0 S 0.148 0.041 S 0.413 0.141 T 233 19845 SENSE 1.242 0 S 0.148 0.051 T 0.479 0.016 S 239 19850 SENSE 1.234 0 S 0.217 0.015 S 1.883 0.001 S 237 19981 SENSE 1.406 0 S 0.36 0 S 2.199 0 S 220 71546 SENSE 1.496 0 S 0.24 0.016 S 0.313 0.052 T 246 71556 SENSE 1.394 0 S 0.26 0.015 S 0.194 0.076 T 276 73029 SENSE 0.88 0.002 S 0.115 0.061 T 0.092 0.105 T 318 74125 SENSE 0.988 0 S 0.171 0.058 T 0.206 0.053 T 283 74329 SENSE 1.19 0 S 0.124 0.08 T 0.043 0.239 / 329 74402 SENSE 1.407 0 S 0.291 0.019 S 0.181 0.087 T 335 74503 SENSE 1.159 0 S 0.171 0.019 S 0.206 0.02 S 340 74553 SENSE 1.141 0 S 0.184 0.02 S 0.704 0.03 S 299 74669 SENSE 1.105 0 S 0.133 0.049 S 0.051 0.362 / 352 74903 SENSE 1.167 0 S 0.168 0.096 T 0.836 0.041 S 362 74980 SENSE 1.084 0 S 0.165 0.027 S 1.07 0.033 S 364 75337 SENSE 1.695 0 S 0.216 0.009 S 0.369 0.072 T 367 75352 SENSE 1.342 0 S 0.198 0.003 S 0.311 0.053 T 370 75358 SENSE 1.314 0 S 0.131 0.034 S 0.012 0.365 / 384 75409 SENSE 1.264 0 S 0.172 0.041 S 0.716 0.039 S 386 75550 SENSE 1.117 0 S 0.18 0.032 S 0.384 0.074 T 400 75571 SENSE 1.182 0 S 0.185 0.042 S 0.496 0.088 T 404 75909 SENSE 1.264 0 S 0.237 0.021 S −0.01 1 / S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

Salt Stress Tolerance Screen

This screen identified genes for recombinant DNA that imparts enhanced salt tolerance, a surrogate for enhanced water use efficiency, as shown in Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.

T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m². On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C. et. al. (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L. Table 6 provides a list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants

TABLE 6 Seedling Root Root Weight Length at Length at Growth at day14 day 11 day 14 Stage Pep Construct p- p- p- RS p- SEQ ID id Orientation delta value c delta value c delta value c mean vallue c 228 19617 SENSE 0.662 0.023 S 0.211 0.138 T 0.019 0.845 / 0.467 0.06 T 229 19750 SENSE 0.794 0.001 S 0.324 0.035 S 0.192 0.001 S 3.409 0.001 S 240 19942 SENSE 0.496 0.022 S 0.123 0.294 / 0.103 0.208 / 1.302 0.103 T 270 72743 SENSE 0.522 0.043 S 0.018 0.856 / 0.194 0.004 S 0.651 0.055 T 278 72920 SENSE 0.377 0.033 S 0.251 0.001 S 0.133 0.004 S 0.191 0.233 / 315 73516 SENSE 0.41 0.005 S 0.079 0.292 / 0.034 0.372 / 1.252 0.053 T 263 74237 SENSE 0.711 0.002 S 0.18 0.135 T 0.187 0.066 T 2.74 0.01 S 282 74327 SENSE 0.554 0.006 S 0.169 0.056 T 0.162 0.005 S 1.469 0.005 S 291 74366 SENSE 0.623 0.008 S 0.125 0.228 / 0.108 0.248 / 0.695 0.062 T 335 74503 SENSE 0.666 0.002 S 0.258 0.027 S 0.103 0.221 / 2.431 0.01 S 336 74504 SENSE 0.976 0.001 S 0.356 0.013 S 0.261 0 S 3.178 0.001 S 296 74622 SENSE 1.092 0.003 S 0.261 0.005 S 0.217 0.013 S 1.457 0.065 T 297 74628 SENSE 0.423 0.057 T −0.062 0.725 / 0.226 0.02 S 0.087 0.31 / 301 74647 SENSE 0.161 0.442 / −0.083 0.569 / 0.208 0.001 S 0.573 0.043 S 352 74903 SENSE 0.446 0.009 S 0.001 0.99 / 0.116 0.034 S 1.234 0.05 T 357 74977 SENSE 0.496 0.019 S 0.2 0.012 S 0.198 0 S 0.764 0.043 S 363 74993 SENSE 0.379 0.017 S 0.242 0.075 T 0.108 0.07 T 0.163 0.319 / 366 75316 SENSE 0.475 0.078 T 0.287 0.002 S 0.178 0.011 S 4 0 S 364 75337 SENSE 0.934 0.004 S 0.217 0.124 T 0.314 0.002 S 1.831 0.013 S 378 75431 SENSE 0.429 0.083 T 0.076 0.397 / 0.096 0.271 / 0.522 0.121 T 379 75455 SENSE 0.286 0.281 / 0.314 0.001 S 0.221 0.006 S 0.396 0.095 T 372 75463 SENSE 0.601 0.011 S 0.141 0.221 / 0.163 0.049 S 1.252 0.058 T 394 75543 SENSE 0.396 0.042 S 0.136 0.054 T 0.088 0.192 T 1.426 0.078 T S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset examined compared to the reference in the current dataset

Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen

There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are potentially useful agronomic traits for improving the germination and growth of crop plants under drought stress. This screen identified genes for recombinant DNA that imparts enhance osmotic stress tolerance, a surrogate for enhanced water use efficiency, as shown in Arabidopsis seed when PEG was used to induce osmotic stress on germinating transgenic lines of seeds.

T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½×MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e. at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.

Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L. Table 7 provides a list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants.

TABLE 7 Seedling Root Root Weight Length at Length at Growth at day14 day 11 day14 Stage Pep p- p- p- RS p- SEQ ID Gene Orientation delta value c delta value c delta value c mean value c 275 10180 ANTI-SENSE 0.322 0.024 S 0.154 0.112 T 0.077 0.233 / 2.679 0.014 S 210 12919 SENSE 0.523 0.001 S 0.15 0.104 T 0.134 0.211 / 1.067 0.084 T 218 16004 ANTI-SENSE 0.58 0.005 S 0.109 0.465 / 0.137 0.048 S 0.96 0.183 T 243 19705 SENSE 0.415 0.098 T 0.225 0.014 S 0.185 0.104 T 2.87 0.009 S 244 19737 SENSE 0.71 0.065 T 0.163 0.454 / 0.127 0.477 / 2.147 0.036 S 238 19757 SENSE 0.876 0.006 S 0.095 0.477 / 0.173 0.016 S 2.298 0.019 S 236 19902 SENSE 0.635 0.012 S 0.233 0.044 S 0.1 0.104 T 2.314 0.016 S 230 19964 SENSE 0.421 0.002 S 0.313 0.027 S 0.388 0.004 S 2.051 0.038 S 247 71330 SENSE 0.35 0.003 S −0.09 0.453 / 0.137 0.189 T 3.292 0.003 S 220 71546 SENSE 0.892 0.003 S 0.32 0.005 S 0.266 0.028 S 3.207 0.005 S 310 73480 SENSE 0.257 0.053 T 0.12 0.058 T 0.069 0.487 / 3.231 0.004 S 254 73651 SENSE 0.581 0.04 S 0.053 0.73 / 0.034 0.609 / 2.992 0.004 S 252 73685 SENSE 0.467 0.024 S 0.137 0.171 T 0.006 0.933 / 1.556 0.026 S 262 73769 SENSE 0.532 0.005 S 0.243 0.073 T 0.043 0.7 / 2.939 0.02 S 284 74340 SENSE 0.56 0.003 S 0.258 0.049 S 0.237 0.036 S 3.541 0 S 293 74374 SENSE 0.587 0.081 T 0.361 0.011 S 0.251 0.009 S 3.001 0.003 S 336 74504 SENSE 0.801 0.003 S 0.185 0.021 S 0.111 0.021 S 4 0 S 337 74528 SENSE 0.552 0.026 S 0.107 0.338 / −0.112 0.418 / 4 0 S 341 74554 SENSE 0.726 0.001 S 0.337 0.012 S 0.224 0.065 T 3.462 0.001 S 343 74590 SENSE 0.511 0.034 S 0.067 0.671 / 0.052 0.753 / 2.479 0.029 S 289 74608 SENSE 0.448 0.043 S 0.175 0.298 / 0.241 0.109 T 2.617 0.016 S 300 74670 SENSE 0.855 0 S 0.154 0.059 T −0.063 0.447 / 2.331 0.013 S 355 74951 SENSE 0.558 0.009 S 0.488 0.003 S 0.517 0.001 S 3.302 0.003 S 363 74993 SENSE 0.677 0 S 0.147 0 S 0.028 0.499 / 3.211 0.005 S 376 75418 SENSE 0.339 0.06 T 0.023 0.763 / 0.263 0.016 S 0.811 0.246 / 381 75456 SENSE 0.43 0.044 S 0.23 0.03 S 0.198 0.003 S 2.674 0.004 S 383 75492 SENSE 0.434 0.018 S 0.073 0.024 S 0.09 0.093 T 0.955 0.186 T 402 75536 SENSE 0.214 0.066 T 0.146 0.015 S 0.221 0.025 S −1.33 0.996 / 389 75564 SENSE 0.407 0.043 S 0.053 0.623 / 0.074 0.569 / 1.839 0.058 T 395 75567 SENSE 0.44 0.02 S −0.077 0.522 / −0.107 0.291 / 2.4 0.034 S 393 75590 SENSE 0.431 0.006 S 0.21 0.022 S 0.195 0.014 S 2.848 0.006 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

Cold Shock Tolerance Screen

This screen identified genes for recombinant DNA that imparts enhanced sold tolerance as shown in Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.

Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing ½× Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, i.e. day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. Table 8 provides a list of recombinant nucleotides that improve cold shock stress tolerance in plants.

TABLE 8 difference rosette in rosette rosette area at area between day Pep area at day 8 day 28 28 and day 8 SEQ ID Construct_id Orientation Delta p-value c delta p-value c delta p-value c 209 13222 SENSE −0.562 0.978 / 0.396 0.074 T 0.581 0.058 T 216 14837 SENSE −0.08 0.661 / 1.007 0.002 S 1.154 0.002 S 212 14841 SENSE 0.662 0.023 S 1.026 0.001 S 1.088 0.004 S 231 19814 SENSE 0.38 0.008 S 0.328 0.027 S 0.55 0.01 S 234 71072 SENSE −0.054 0.58 / 0.736 0.005 S 0.662 0.027 S 224 71148 SENSE −0.43 0.899 / 0.189 0.14 T 0.643 0.02 S 217 71253 SENSE 0.318 0.004 S 0.442 0.019 S 0.54 0.009 S 251 71689 SENSE −0.566 0.907 / 0.62 0.01 S 0.879 0.043 S 312 73513 SENSE 0.48 0.009 S 0.61 0.022 S 0.439 0.074 T 314 73527 SENSE 0.499 0.034 S 0.9 0.001 S 1.087 0.001 S 321 74115 SENSE 0.254 0.17 T 0.896 0.002 S 1.029 0.002 S 324 74165 SENSE 0.142 0.28 / 0.293 0.115 T 0.61 0.018 S 286 74345 SENSE −0.109 0.746 / 0.819 0.004 S 1.148 0.009 S 333 74418 SENSE 0.421 0.002 S 1.012 0.003 S 0.565 0.038 S 337 74528 SENSE 0.395 0.004 S 0.544 0.018 S 0.725 0.009 S 294 74618 SENSE 0.274 0.003 S 0.781 0.011 S 0.941 0.033 S 305 74685 SENSE −0.238 0.923 / 0.758 0.001 S 1.076 0 S 360 74919 SENSE 0.221 0.214 / 0.358 0.053 T 0.388 0.108 T 356 74940 SENSE 0.28 0.143 T 0.903 0.001 S 0.952 0.002 S 358 74954 SENSE 0.197 0.176 T 0.602 0.013 S 0.712 0.024 S 364 75337 SENSE 0.669 0.002 S 0.695 0.002 S 0.603 0.014 S 381 75456 SENSE 0.413 0.034 S 0.895 0.002 S 0.998 0 S 380 75491 SENSE 0.324 0.047 S 0.914 0.001 S 1.11 0.001 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.

Cold Germination Tolerance Screen

This screen identified genes for recombinant DNA that imparts enhanced cold tolerance as shown in Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.

T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of ½× Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m²/s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.

The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. Table 9 provides a list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants.

TABLE 9 Root Length Growth Stage Pep at day 28 at day 28 SEQ ID Construct_id Orientation delta p-value c RS mean p-value c 269 10814 ANTI-SENSE 0.218 0.009 S 3.148 0.007 S 208 17465 SENSE 0.269 0.027 S 3.246 0.004 S 223 17919 SENSE 0.366 0.002 S 4 0 S 346 18020 SENSE 0.112 0.105 T 3.016 0.014 S 406 18026 SENSE 0.407 0.002 S 2.111 0.039 S 226 18844 SENSE 0.464 0.012 S 2.927 0.005 S 225 19647 SENSE 0.479 0.002 S 3.129 0.008 S 232 19720 SENSE 0.295 0.003 S 4 0 S 229 19750 SENSE 0.224 0.006 S 3.161 0.006 S 245 19812 SENSE 0.261 0.002 S 3.022 0.014 S 235 19949 SENSE 0.226 0 S 3.093 0.01 S 220 71546 SENSE 0.3 0.001 S 3.181 0.006 S 274 73061 SENSE 0.306 0.002 S 3.447 0.001 S 256 73271 SENSE 0.062 0.209 / 4 0 S 257 73282 SENSE 0.216 0.023 S 4 0 S 255 73342 SENSE 0.366 0 S 4 0 S 292 74383 SENSE 0.182 0.019 S 4 0 S 336 74504 SENSE 0.368 0.001 S 4 0 S 337 74528 SENSE 0.202 0 S 4 0 S 339 74541 SENSE 0.338 0.002 S 4 0 S 341 74554 SENSE 0.239 0.001 S 4 0 S 342 74578 SENSE 0.53 0 S 4 0 S 289 74608 SENSE 0.261 0.003 S 4 0 S 351 74880 SENSE 0.21 0.04 S 2.977 0.017 S 359 74907 SENSE 0.253 0.004 S 1.951 0.096 T 372 75463 SENSE 0.467 0.002 S 4 0 S 373 75475 SENSE 0.307 0.009 S 3.496 0 S 382 75480 SENSE 0.268 0.012 S 2.955 0.018 S 392 75554 SENSE 0.149 0.039 S 4 0 S 395 75567 SENSE 0.236 0.003 S 4 0 S 347 75850 SENSE 0.616 0 S 3.053 0.002 S 348 75861 SENSE 0.272 0.001 S 4 0 S 349 75875 SENSE 0.138 0.066 T 4 0 S 403 75991 SENSE 0.038 0.296 / 2.667 0.051 T S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

Shade Tolerance Screen

Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes may confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response may be associated with higher yields. Genes that favor growth under low light conditions may also promote yield, as inadequate light levels frequently limit yield. This screen identified genes for recombinant DNA that imparts enhanced shade tolerance in Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.

T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½ X MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m²/s, far/red ratio (655/665/725/735) ˜0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.

Table 10 provides a list of recombinant DNA constructs that improve shade tolerance in plants

TABLE 10 Number of Petiole length at seedling weight Leaf angle at rosette leaves at day 23 day 23 day 23 day 23 Pep p- p- RS p- RS p- SEQ ID Construct_id Orientation delta value c delta value c mean value c mean value c 407 11810 ANTI- −0.138 0.03 S 0.158 0.245 / 0.246 0.296 / −0.1 0.822 / SENSE 267 16014 SENSE −0.267 0.012 S −1.129 0.015 / 0.042 0.425 / 0.773 0.209 / 249 71571 SENSE −0.548 0.005 S −0.212 0.177 / 0.325 0.224 / 0.611 0.22 / 273 72984 SENSE −0.219 0.064 T −0.126 0.178 / 0.12 0.315 / 0.476 0.28 / 280 73044 SENSE −0.722 0.083 T −0.572 0.173 / −0.032 1 / −1.35 0.992 / 307 73476 SENSE −0.01 0.905 / 0.103 0.354 / 0.739 0.177 T 1.896 0.053 T 311 73482 SENSE −0.394 0.107 T −0.095 0.611 / 0.045 0.375 / 0.252 0.376 / 306 73487 SENSE 0.064 0.457 / −0.131 0.583 / 1.656 0.051 T 1.131 0.15 T 261 74306 SENSE −1.107 0.13 T −1.924 0.116 / 0.291 0.261 / −0.103 0.591 / 282 74327 SENSE 0.029 0.777 / 0.105 0.762 / 0.666 0.12 T 1.252 0.116 T 330 74476 SENSE −0.092 0.072 T −0.613 0.107 / 0.271 0.246 / −0.026 0.511 / S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.

Early Plant Growth and Development Screen

This screen identified genes for recombinant DNA that imparts enhanced early plant growth and development, a surrogate for increased yield, as shown in Arabidopsis plants examined in a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.

T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m²/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.

Table 11 provides a list recombinant DNA constructs that improve early plant growth and development.

TABLE 11 Root Length at Root Length at day 10 day 14 Seedling Weight Pep p- p- p- SEQ ID Construct_id Orientation delta value c delta value c delta value c 213 13478 ANTI- 0.242 0.062 T 0.159 0.075 T 0.603 0.013 S SENSE 227 19525 SENSE 0.249 0.183 T 0.245 0.001 S 0.385 0.062 T 221 70109 SENSE 0.282 0.001 S 0.23 0.001 S 0.564 0 S 248 71332 SENSE 0.071 0.548 / 0.093 0.17 T 0.419 0.009 S 220 71546 SENSE 0.307 0.057 T 0.231 0.013 S 0.561 0.006 S 246 71556 SENSE 0.408 0.008 S 0.291 0.011 S 0.328 0.263 / 408 72418 SENSE 0.144 0.063 T 0.17 0 S 0.46 0.006 S 253 72636 SENSE 0.486 0.026 S 0.339 0 S 0.705 0.006 S 279 72957 SENSE 0.228 0.053 T 0.158 0.089 T 0.371 0.08 T 309 73418 SENSE 0.242 0.082 T 0.148 0.089 T 0.212 0.085 T 316 73530 SENSE 0.239 0.023 S 0.17 0.003 S 0.442 0.001 S 313 73550 SENSE 0.181 0.046 S 0.113 0.016 S 0.304 0.045 S 259 73913 SENSE 0.243 0.069 T 0.091 0.26 / 0.452 0.015 S 325 74106 SENSE 0.257 0.003 S 0.192 0.015 S 0.34 0.052 T 318 74125 SENSE 0.104 0.549 / 0.139 0.048 S 0.524 0.002 S 320 74126 SENSE 0.149 0.082 T 0.065 0.284 / 0.354 0.127 T 322 74127 SENSE 0.381 0 S 0.212 0.006 S 0.63 0.002 S 323 74128 SENSE 0.213 0.091 T 0.12 0.161 T 0.541 0.002 S 326 74130 SENSE 0.14 0.002 S 0.144 0.001 S 0.003 0.955 / 327 74132 SENSE 0.134 0.275 / 0.144 0.049 S 0.336 0.025 S 328 74144 SENSE 0.137 0.217 / 0.134 0.065 T 0.492 0.012 S 319 74161 SENSE 0.205 0.02 S 0.131 0.018 S 0.459 0.035 S 263 74237 SENSE 0.253 0 S 0.189 0.002 S 0.408 0.013 S 265 74256 SENSE 0.28 0.04 S 0.202 0.012 S 0.461 0.034 S 260 74305 SENSE 0.184 0.063 T 0.131 0.026 S 0.257 0.121 T 281 74323 SENSE 0.13 0.08 T 0.067 0.054 T 0.426 0.005 S 285 74341 SENSE 0.185 0.044 S 0.07 0.106 T 0.144 0.191 T 293 74374 SENSE 0.103 0.187 T 0.171 0.008 S 0.518 0.023 S 302 74385 SENSE 0.051 0.461 / −0.043 0.693 / 0.214 0.098 T 303 74386 SENSE 0.211 0.12 T 0.136 0.092 T 0.081 0.616 / 304 74387 SENSE 0.11 0.528 / 0.17 0.052 T 0.378 0.027 S 350 74548 SENSE 0.169 0.041 S 0.09 0.046 S 0.336 0.08 T 288 74604 SENSE 0.157 0.231 / 0.181 0.014 S 0.586 0.001 S 290 74609 SENSE 0.24 0.029 S 0.102 0.227 / 0.457 0.014 S 287 74616 SENSE 0.192 0.047 S 0.137 0.125 T 0.286 0.204 / 295 74619 SENSE 0.181 0.415 / 0.153 0.149 T 0.448 0.056 T 296 74622 SENSE 0.083 0.481 / 0.071 0.331 / 0.311 0.076 T 298 74631 SENSE 0.203 0.02 S 0.115 0.019 S −0.049 0.633 / 353 74915 SENSE 0.202 0.004 S 0.136 0.027 S 0.409 0.012 S 354 74927 SENSE 0.103 0.148 T 0.117 0.021 S 0.319 0.056 T 356 74940 SENSE 0.127 0.001 S 0.117 0.049 S 0.344 0.028 S 371 75312 SENSE 0.191 0.055 T 0.155 0.006 S 0.526 0.001 S 365 75339 SENSE 0.168 0.029 S 0.031 0.704 / 0.21 0.208 / 374 75440 SENSE 0.15 0.037 S 0.059 0.566 / −0.039 0.923 / 372 75463 SENSE 0.392 0.006 S 0.284 0.011 S 0.432 0.15 T 375 75488 SENSE 0.101 0.289 / 0.083 0.113 T 0.444 0.003 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

Late Plant Growth and Development Screen

This screen identified genes for recombinant DNA that imparts enhanced late plant growth and development, a surrogate for increased yield, as shown in Arabidopsis plants examined in a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.

Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft³. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ˜5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 μmoles/m²/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.

Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.

The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.

Table 12 provides a list of recombinant DNA constructs that improve late plant growth and development.

TABLE 12 Rosette Dry Silique Dry Weight Rosette Radius Seed Dry Weight Weight Silique Length Pep Construct p- p- p- p- p- SEQ ID id delta value c delta value c Delta value c delta value c delta value c 213 13478 0.054 0.365 / 0.217 0.013 S 0.052 0.347 / 0.293 0.084 T 0.079 0.021 S 241 19787 0.233 0.052 T 0.067 0.022 S 0.66 0.019 S −0.02 0.75 / 0.06 0.006 S 268 72751 0.287 0.012 S −0.141 0.714 / −0.991 0.973 / 0.094 0.099 T −0.024 0.675 / S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.5) T: represents the transgenic plants showed a trend of trait improvement compared to the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

Limited Nitrogen Tolerance Screen

Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This screen identified genes for recombinant DNA that imparts enhanced nitrogen use efficiency as shown in Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.

T2 seeds were plated on glufosinate selection plates containing 0.5×N-Free Hoagland's T 0.1 mM NH₄NO₃ T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e. viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L. The leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system. A statistical logistic regression model was developed to predict an overall value based on five colors for each plant.

Table 13 provides a list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants.

TABLE 13 Number of green leaves leaf color Root Length Rosette Weight Pep Construct RS p- p- RS p- p- SEQ ID id mean value c delta value c mean value c delta value c 334 10150 1.496 0.007 S 0.974 0.007 S −0.285 0.022 / −0.024 0.572 / 222 10335 0.993 0.014 S 0.953 0.01 S −0.359 0 / −0.057 0.122 / 277 11145 0.368 0.41 / 1.059 0.004 S −0.141 0.211 / −0.086 0.143 / 361 11735 0.522 0.554 / 1.132 0.003 S −0.134 0.147 / 0.082 0.001 S 206 12030 0.57 0.321 / 0.944 0.027 S −0.28 0.005 / −0.031 0.545 / 368 12189 0.134 0.791 / 0.76 0.034 S −0.147 0.024 / −0.082 0.099 / 308 73465 0.591 0.195 T 0.586 0.061 T −0.03 0.631 / −0.04 0.249 / 328 74144 0.845 0.069 T 1.021 0.003 S 0.181 0.04 S 0.028 0.481 / 331 74417 1.051 0.021 S 1.4 0.001 S −0.155 0.019 / −0.071 0.16 / 338 74588 0.484 0.31 / 1.059 0.01 S −0.101 0.167 / −0.051 0.608 / 369 75321 0.607 0.041 S 0.317 0.423 / −0.095 0.238 / 0.056 0.021 S 377 75419 −0.779 0.198 / 0.635 0.019 S −0.116 0.024 / 0.009 0.795 / 385 75424 −0.354 0.537 / 1.489 0 S −0.245 0.003 / −0.062 0.165 / 391 75506 0.969 0 S 0.588 0.049 S 0.081 0.108 T −0.026 0.545 / 388 75528 −0.026 0.932 / 0.229 0.594 / −0.042 0.534 / 0.111 0.058 T 396 75544 0.197 0.369 / 1.033 0.006 S −0.283 0.034 / −0.134 0.021 / 398 75546 0.577 0.001 S 1.108 0.002 S −0.321 0.006 / 0.01 0.765 / 390 75553 −0.182 0.643 / 0.425 0.058 T −0.104 0.12 / −0.096 0.104 / 397 75556 0.766 0.01 S −0.544 0.179 / 0 1 / 0.271 0 S 399 75558 0.343 0.406 / 0.861 0.008 S −0.102 0.035 / −0.106 0.003 / 387 75575 0.087 0.83 / 1.147 0.001 S −0.117 0.093 / −0.03 0.325 / 401 75583 −0.621 0.399 / −0.166 0.595 / −0.01 0.906 / 0.162 0.002 S 344 75834 0.425 0.038 S 0.589 0.03 S −0.067 0.343 / 0.028 0.429 / 345 75835 0.486 0.266 / 0.228 0.499 / −0.16 0.026 / 0.159 0 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared than the reference with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

Statistic Analysis for Qualitative Responses

Table 14 provides a list of responses that were analyzed as qualitative responses

TABLE 14 response screen categories (success vs. failure) wilting response Risk Soil drought tolerance screen non-wilted vs. wilted Score growth stage at day 14 heat stress tolerance screen 50% of plants reach stage1.03 vs. not growth stage at day 14 salt stress tolerance screen 50% of plants reach stage1.03 vs. not growth stage at day 14 PEG induced osmotic stress tolerance 50% of plants reach stage1.03 vs. not screen growth stage at day 7 cold germination tolerance screen 50% of plants reach stage 0.5 vs. not number of rosette leaves Shade tolerance screen 5 leaves appeared vs. not at day 23 flower bud formation at Shade tolerance screen flower buds appear vs. not day 23 leaf angle at day 23 Shade tolerance screen >60 degree vs. <60 degree number of green leaves at limited nitrogen tolerance screen 6 or 7 leaves appeared vs. not day 21 number of rosette leaves limited nitrogen tolerance screen 6 or 7 leaves appeared vs. not at day 21 Flower bud formation at limited nitrogen tolerance screen flower buds appear vs. not day 21

Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 16. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log₂ ^(RR). Subsequently the risk scores from multiple events for each transgene of interest were evaluated for statistical significance by t-test using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.

Statistic Analysis for Quantitative Responses

Table 15 provides a list of responses that were analyzed as quantitative responses.

TABLE 15 response screen seed yield Soil drought stress tolerance screen seedling weight at day 14 heat stress tolerance screen root length at day 14 heat stress tolerance screen seedling weight at day 14 salt stress tolerance screen root length at day 14 salt stress tolerance screen root length at day 11 salt stress tolerance screen seedling weight at day 14 PEG induced osmotic stress tolerance screen root length at day 11 PEG induced osmotic stress tolerance screen root length at day 14 PEG induced osmotic stress tolerance screen rosette area at day 8 cold shock tolerance screen rosette area at day28 cold shock tolerance screen difference in rosette area cold shock tolerance screen from day 8 to day 28 root length at day 28 cold germination tolerance screen seedling weight at day 23 Shade tolerance screen petiole length at day 23 Shade tolerance screen root length at day 14 Early plant growth and development screen Seedling weight at day14 Early plant growth and development screen Rosette dry weight at day Late plant growth and development screen 53 rosette radius at day 25 Late plant growth and development screen seed dry weight at day 58 Late plant growth and development screen silique dry weight at day 53 Late plant growth and development screen silique length at day 40 Late plant growth and development screen Seedling weight at day 21 Limited nitrogen tolerance screen Root length at day 21 Limited nitrogen tolerance screen

The measurements (M) of each plant were transformed by log₂ calculation. The Delta was calculated as log₂M(transgenic)−log₂M(reference). Subsequently the mean delta from multiple events of the transgene of interest was evaluated for statistical significance by t-test using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). The Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. The Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.

EXAMPLE 2

This example illustrates the identification of homologs of the cognate proteins of the genes identified as imparting an enhanced trait.

A BLAST searchable “All Protein Database” was constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a DNA sequence provided herein was obtained, an “Organism Protein Database” was constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.

The All Protein Database was queried using amino acid sequence of cognate protein for gene DNA used in trait-improving recombinant DNA, i.e. sequences of SEQ ID NO: 205 through SEQ ID NO: 408 using “blastp” with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.

The Organism Protein Database was queried using amino acid sequences of SEQ ID NO: 205 through SEQ ID NO: 408 using “blastp” with E-value cutoff of 1e-4. Up to 1000 top hits were kept. A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e-8. The hit with the best E-value was compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 409 to SEQ ID NO: 19247. These orthologs are reported in Tables 2 as homologs to the proteins cognate to genes used in trait-improving recombinant DNA.

TABLE 2 SEQ ID NO: homolog SEQ ID NOs 206: 9461 19072 14856 5315 7726 11678 8466 4567 9541 4039 2736 826 4434 18755 7163 19021 16621 18594 207: 11732 5088 14017 14658 8659 17828 14150 11838 7420 577 13978 3089 9378 8177 5473 4151 15455 3299 3397 17568 12473 2946 17428 3126 15408 3997 18806 10067 3246 19105 208: 11715 12490 18003 15562 5946 18565 5550 13362 1866 4207 6966 6785 16958 17740 12495 9774 3632 7059 937 10643 12198 6865 13806 1023 12708 14552 16746 18201 16712 7735 209: 3105 15418 1368 15360 5654 7902 3038 16108 14416 16444 10078 17851 12848 15183 12997 18090 18617 1312 16630 4080 4082 7689 19205 17262 13305 5780 10544 14798 16363 16166 17737 210: 17539 13894 15187 11374 17968 9384 7645 13991 5852 211: 16101 13052 9940 10298 9899 15964 10104 18651 6853 12619 1551 4764 684 13219 15864 9975 3261 4237 2710 18739 15477 7248 582 15025 212: 11577 10930 12130 13904 13619 10462 9686 10796 9854 12277 14708 4822 437 6953 7206 9936 2948 7987 13119 2409 213: 11281 4744 9418 8607 3777 4299 2607 2319 7251 7279 9577 14778 18625 6286 4491 14417 1831 7825 8703 3214 17914 10229 11951 17625 970 966 7114 17802 17749 17813 17788 17783 17787 17765 17808 17806 17764 17726 17746 17810 17834 17732 17745 17767 17728 17730 17744 17747 17781 2457 15330 15328 7187 1588 17923 1156 5341 16738 11147 11237 10534 13932 6444 2913 14896 13736 10170 11594 17581 1429 12223 7798 16703 10946 10966 10944 10961 10934 11706 11679 11677 11704 3305 1863 17474 15572 4795 6459 794 8522 15354 13706 8632 5186 8156 7182 1057 12383 18370 18371 12218 14763 6085 9619 6084 3613 11617 15462 4013 14623 13880 3030 1260 16762 11244 3082 9189 11858 14221 19035 2439 4014 1840 8134 16791 14100 8244 8347 15753 6777 10859 2830 16405 8205 13954 11632 18494 11891 2663 1366 18247 15522 10282 14126 10940 8802 12556 997 3391 4295 7548 5823 17340 5932 2459 10562 14935 17104 15135 2045 2256 14248 15748 638 11436 10293 14019 12831 7142 6143 5949 14114 17359 10556 13121 2699 12459 3820 10865 15441 5257 8413 14080 10255 12573 772 6606 3642 8804 3457 1348 16022 7874 5815 15304 598 3258 3259 1401 4197 4837 5770 9990 11860 5998 13653 19240 18528 798 5714 7362 5197 13400 6454 4954 587 15889 1391 1208 2577 2564 4704 4774 5289 11843 15452 3750 18789 950 13589 16248 18822 15416 9549 8091 2839 2840 16123 8406 8410 15495 1886 15489 18634 15405 8526 8546 8530 11309 10415 12157 12164 12160 12156 18974 9416 10400 9468 6180 6183 17850 11085 6361 1846 9141 7414 12282 2648 18663 16836 2696 12925 19084 7529 7271 9600 16269 8179 15909 8971 14368 11123 15003 7928 18412 13507 8354 2167 8528 8545 13622 11823 5877 9383 18047 12323 7126 13778 15775 6818 14349 1843 1841 5467 18619 2511 13117 12441 18799 4847 4844 4846 1482 1029 13661 9950 7913 18555 13411 12291 15118 13667 11824 17679 15097 13368 4611 15383 5294 5297 5295 10809 6024 13660 13664 18078 18063 18075 18080 18064 18061 2901 2896 11461 9567 2623 15619 13681 16483 19066 18430 14575 17264 14824 16907 3361 3539 9690 9562 13782 14476 16298 672 4789 18071 16409 11810 9328 15142 16658 19113 15890 11168 14282 7337 2737 18782 2977 6021 6936 15780 15779 14381 3119 8277 5647 3188 5391 2197 8529 16229 4706 11648 18333 12351 10590 4964 12869 12571 17461 15151 2108 12256 13689 6178 11145 10127 14620 521 12494 9664 13352 18819 17275 16855 6094 16051 1861 1543 17278 3184 3785 7977 10869 14020 1073 8390 13292 3685 12532 3942 3338 7643 5224 7941 17062 4374 17281 15560 18682 6397 9485 11017 18260 11733 7788 6676 7371 15931 2677 1855 7550 12942 16195 2434 13586 14216 2671 18036 5925 11102 2387 3968 15553 12886 12211 6446 13317 15962 2965 6866 2247 2576 18624 13803 8821 12537 18487 2386 15498 10683 8191 15227 10351 14762 14780 14761 1568 1570 1823 11984 13721 7268 10834 14940 2764 6670 1577 8050 4950 17318 17533 743 1273 13143 2621 6532 6553 10775 11080 10240 6827 13829 14551 14376 8122 11203 11186 9158 4943 11793 4606 4451 4941 4925 4421 4923 4447 4439 13094 16831 5632 16842 7972 8319 4463 18291 1153 5593 14256 15648 10411 15778 3836 8646 11057 10802 2547 10675 10705 12481 17144 11933 9742 760 816 2393 15797 15801 4227 10125 15598 14171 4499 16812 14907 3633 2579 6096 11005 214: 17205 12417 5182 11592 1218 18584 9104 3562 17644 15108 2456 12621 2781 16359 2519 11488 17691 5523 3592 4365 17685 18564 9255 3981 17471 14932 6896 17261 14309 4464 215: 11565 17980 9870 6731 7560 8022 11032 6899 11020 17043 17521 13209 6078 3756 6314 4852 7764 17958 8539 3600 2654 15211 8089 10817 882 2355 12320 10576 857 216: 4548 1814 1811 18872 5005 8334 4062 18447 18595 217: 10206 9379 12609 7556 16810 18633 7572 6772 9785 18400 4394 8373 3586 13142 13290 11170 2118 4015 4419 3154 4988 15178 2746 16499 7153 17079 12443 9989 7666 3147 16089 8157 15468 13125 13112 1739 16612 16627 16628 7970 218: 14011 6366 12194 19166 14872 8536 9025 15878 5246 1466 10734 18375 19051 3284 11851 1926 16644 15376 15389 19007 13011 16761 14930 17632 17097 11908 10938 10056 5151 1836 696 16029 14064 3132 16092 16678 14296 5107 9978 12711 18145 4922 219: 1266 12114 9582 1006 14040 2995 2574 14277 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8129 10993 5337 2955 10550 1632 4698 18308 13085 15485 13327 16105 389: 2476 3590 2914 12550 12552 7501 14570 15819 11167 4325 19077 6830 4556 10406 12930 5172 5060 12389 3569 16656 5168 9775 14074 17762 9431 2976 16817 11358 11360 2041 11375 10922 11355 11359 14965 10920 10918 3529 4796 11740 2289 15427 7180 9275 4129 7616 13151 18966 10689 14083 6228 2080 13696 5628 10009 411 10499 15596 8605 17387 390: 13101 8214 18411 6355 17130 17131 17112 17106 11037 5175 5207 16634 16638 18236 18250 13007 12625 10843 10358 4002 905 7460 17283 10362 10388 10845 13303 2314 12875 17641 7106 16084 4137 9491 4494 14185 14189 14160 13722 10262 9561 10261 2652 16419 14234 3867 3394 4122 16608 17323 18139 16832 11596 16537 14193 14190 14231 14212 17832 7504 18708 7840 16675 16237 7108 13984 2646 18664 14232 8358 12918 4473 4497 431 13345 11107 14988 10858 8415 10522 18463 2013 10896 13582 1453 8762 16443 14346 11683 2065 10233 10846 10363 10391 10393 14422 9935 17273 17249 8363 10121 14942 391: 7780 7778 5749 16030 8501 14291 14288 6980 8600 7808 14360 14094 2039 3393 16652 5033 5164 14882 16247 4249 12196 17478 5851 448 19005 392: 9293 16557 723 6692 9622 2591 13628 6928 1592 393: 5309 16676 1992 5415 17277 4097 6941 16134 3966 10723 12275 12413 9592 394: 10929 8533 15300 1943 2871 3355 8440 1643 4780 15402 10696 4627 2660 3426 1295 1614 466 18055 18870 5343 6172 13204 2509 14838 16696 14719 12186 9237 5229 14362 18820 11703 10441 9402 3427 6904 6394 15444 13539 480 4107 3143 11612 16378 9125 5638 5458 4628 12830 16118 11849 7565 14432 395: 17920 6614 14177 8433 18119 14743 1547 2798 4829 13098 1792 7185 5546 12686 17738 14286 17308 15203 7356 15424 8898 10366 396: 1612 16074 15966 6215 9512 6739 712 4754 9542 926 15250 17094 3886 1518 14141 3582 17743 2596 16577 7981 8476 11139 9991 7519 16523 4476 3159 2443 397: 6955 17338 4807 13366 13886 3990 12822 4206 11204 4966 12012 18854 18590 18505 5937 6734 2714 7052 1150 4851 7568 10870 5135 3950 2713 870 17666 8862 972 4428 1180 15407 398: 10762 10763 17831 18710 4571 2491 18826 7281 7980 12839 7132 3515 11431 13508 15105 11150 12370 14765 7924 8625 10099 5689 10100 7454 10434 8719 3324 3759 1396 7985 1985 399: 6493 10378 18309 8131 4746 2656 3568 15048 5685 9021 16845 8807 18908 2035 18616 19229 9844 10776 11514 15103 1336 4804 17204 14756 12584 18287 12312 5524 13410 6108 12653 16440 10889 4657 4508 11491 4103 400: 14710 10682 11646 10632 9092 7695 1867 15667 2172 14920 10057 4313 15838 6000 16168 13497 12464 7428 3227 15903 11817 6518 7230 15193 14479 15307 9534 8999 10201 401: 4269 415 5196 1888 17473 5940 17913 2427 4192 894 2283 3972 4409 4808 15898 14757 16253 13957 402: 8349 2740 7671 12717 5139 12414 4134 7424 16056 14823 403: 1589 17604 12728 8019 2032 1121 5422 4393 814 3576 1329 18252 17534 7522 6755 8555 13532 14465 5342 14260 12366 13545 11833 15130 16303 3048 15435 12548 12465 9395 4550 15303 15548 16379 15934 3788 11207 10866 16567 9796 10597 2843 9814 6036 13084 15810 18073 12289 2610 8431 8133 10743 5277 5274 9812 9270 16062 1410 18832 3278 11379 7651 8619 4074 13579 11278 7552 3482 1921 3110 13040 3715 588 16215 14079 15855 15077 12165 4158 14545 7138 12317 14284 16674 7176 4557 4843 4827 14556 15959 12712 12693 12300 9895 9617 18976 3521 15031 1253 9850 1713 948 17470 9817 8246 14610 14409 4404 18149 18916 3122 6477 11641 5344 5193 15313 4566 4856 6382 6385 8287 13657 6526 12895 13000 17835 5551 4058 4427 6492 3925 15887 6882 13235 2054 11583 8492 7588 15092 977 3464 6674 11033 10561 12912 12978 14142 19136 951 13846 6528 11069 16860 10474 14237 10178 9206 9999 12994 1371 1369 18499 15946 14691 5796 15067 13591 14544 10116 9572 9076 3395 18068 9445 17137 10070 12598 12451 5291 8421 13493 12446 16898 3422 12469 9327 12751 1725 12393 11867 16709 6201 2489 19025 15355 12432 10704 10788 15175 13881 15050 11031 2284 16846 8929 13843 15877 12575 2501 3898 8155 8181 13467 7071 13380 18512 6767 11884 3330 15689 16649 4862 2400 11639 2206 6774 7277 10750 13838 5371 9923 6934 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11937 11215 8917 18762 8922 6629 3169 4418 7255 17978 6392 4006 16582 4177 13299 18105 19050 1884 8982 18462 13743 10049 17020 1107 14164 17443 3211 807 9415 7769 2665 7716 9819 4793 8194 4487 9462 1406 8450 11140 4167 18203 3917 15866 2776 1567 9782 15174 12626 4681 12824 14018 4910 4659 2562 2122 2788 9880 2428 871 8389 7192 16613 2982 3929 11900 8750 5259 18517 14460 1370 18379 7537 11555 4777 12893 14616 15017 5702 12071 2926 2018 2392 18128 17823 17870 13449 12192 1385 8320 11784 8264 14559 5910 11792 8248 1361 17542 1038 17221 1250 12347 10203 15635 7181 7956 13405 1627 10660 3003 6686 18312 14977 2919 13737 1505 4646 9493 11913 9654 14413 16822 11895 12844 7146 17760 12372 14263 18841 10587 16428 18770 12264 16337 14633 11408 17098 2635 7437 18818 16147 17848 15393 9910 6063 5725 6571 5134 17464 10392 6472 17903 405: 3906 4734 13745 7402 14874 764 406: 5355 6984 4667 17305 11490 16367 8426 10381 1464 11818 624 7412 3333 9382 15475 11760 13337 407: 12506 19148 10381 2347 9031 1569 408: 1173 2332 4489

EXAMPLE 3

This example illustrates the construction of a consensus amino acid sequence of homologous proteins of homologous genes that impart an enhanced trait.

ClustalW program was selected for multiple sequence alignments of the amino acid sequence of SEQ ID NO: 406 and 17 homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. Shown in FIG. 1 are the sequences of SEQ ID NO: 406, its homologs and the consensus sequence, as set forth in SEQ ID NO: 19248. The symbols for consensus sequence are (1) uppercase letters for 100% identity in all positions of multiple sequence alignment output; (2) lowercase letters for >=70% identity; symbol; (3) “X” indicated <70% identity; (4) dashes “-” meaning that gaps were in >=70% sequences.

The consensus amino acid sequence can be used to identify DNA corresponding to the full scope of this invention that is useful in providing transgenic plants, for example corn and soybean plants with enhanced agronomic traits, for example improved nitrogen use efficiency, improved yield, improved water use efficiency and/or improved growth under cold stress, due to the expression in the plants of DNA encoding a protein with amino acid sequence identical to the consensus amino acid sequence.

EXAMPLE 4

This example illustrates the identification of amino acid domain by Pfam analysis.

The amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software in the appended computer listing. The Pfam protein families for the proteins of SEQ ID NO: 205 through 408 are shown in Table 16. The Hidden Markov model databases for the identified patent families are also in the appended computer listing allowing identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 214 is characterized by two Pfam domains, i.e. “C1_(—)4” and “Ssl1”. See also the protein with amino acids of SEQ ID NO:222 which is characterized by two copies of the Pfam domain “MatE”. In Table 16 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 17.

TABLE 16 PEP SEQ ID Pfam domain NO name begin stop score E-value 206 zf-A20 10 34 35 2.40E−07 206 zf-AN1 104 144 64.5 3.10E−16 207 Cyclin_N 33 168 12.1 0.00023 208 Gpi16 9 603 1272 0 212 BSD 100 167 44.7 2.80E−10 212 BSD 179 244 67.5 3.90E−17 213 Catalase 18 401 977.7 3.80E−291 214 Ssl1 22 277 646.3 2.20E−191 214 C1_4 361 409 101.1 2.90E−27 215 Bromodomain 119 208 105.8 1.10E−28 216 Pkinase 75 343 −9.1 1.60E−07 217 PTR2 133 544 197.2 3.50E−56 218 FTCD_N 5 195 377.6 1.70E−110 219 Abhydrolase_1 50 272 30.4 3.00E−06 220 HhH-GPD 172 317 88.2 2.30E−23 222 MatE 40 200 121.9 1.60E−33 222 MatE 261 433 96 1.00E−25 224 ubiquitin 48 120 24.7 0.00029 224 BAG 138 219 94.2 3.50E−25 225 Lipase_GDSL 37 365 370.9 1.80E−108 226 DUF231 280 449 234.8 1.60E−67 227 Aldedh 16 485 842 2.80E−250 228 RRM_1 110 181 79.9 7.10E−21 228 RRM_1 214 284 87.8 2.90E−23 229 GATase_2 2 162 10.5 7.60E−12 229 Asn_synthase 211 478 335.9 6.10E−98 230 zf-C2H2 273 295 30.6 5.00E−06 231 HLH 62 113 39 1.50E−08 232 PP2C 39 323 106.9 5.20E−29 233 zf-C3HC4 96 137 33.4 7.10E−07 234 AP2 83 146 144.5 2.60E−40 235 Homeobox 84 145 72.6 1.10E−18 236 zf-C3HC4 87 129 31.8 2.10E−06 237 Acyl_transf_1 52 354 −13.2 6.40E−11 238 Aldo_ket_red 5 292 465.6 5.50E−137 239 adh_short 13 179 55.1 2.00E−13 240 HMG_CoA_synt 5 453 992.9 1.00E−295 241 SRF-TF 9 59 121.8 1.80E−33 241 K-box 75 175 148.8 1.20E−41 242 Ribosomal_S8e 1 237 327.1 2.70E−95 243 zf-C3HC4 103 144 37.8 3.30E−08 244 zf-C2H2 4 26 22.3 0.0015 244 zf-C2H2 204 226 22.4 0.0014 244 zf-C2H2 236 258 20.6 0.005 245 Aa_trans 45 439 358 1.30E−104 246 LEA_4 71 141 15.6 0.05 247 p450 66 499 209.4 7.60E−60 248 p450 40 503 289.8 4.70E−84 249 Phi_1 25 278 515 7.40E−152 250 zf-B_box 3 47 56.2 9.50E−14 251 PP2C 84 348 267.9 1.80E−77 254 Radical_SAM 171 337 77.3 4.40E−20 255 Pkinase 25 283 174.5 2.30E−49 256 adh_short 6 182 42.9 9.80E−10 257 Skp1_POZ 4 64 105.1 1.80E−28 257 Skp1 112 190 173 6.70E−49 258 DPBB_1 73 151 142.6 9.30E−40 258 Pollen_allerg_1 162 239 163.9 3.70E−46 259 LRRNT_2 18 58 40.7 4.40E−09 259 LRR_1 86 108 12.3 1.6 259 LRR_1 109 133 15.7 0.15 259 LRR_1 134 157 17.4 0.047 259 LRR_1 158 177 8.3 11 259 LRR_1 179 202 12.5 1.3 259 Pkinase 334 601 3.8 2.90E−08 260 Methyltransf_11 135 225 25.7 0.00015 261 Ubie_methyltran 34 287 368.5 9.10E−108 261 Methyltransf_11 88 205 70.4 5.00E−18 261 Methyltransf_12 88 203 38.6 1.90E−08 262 MtN3_slv 11 100 69.4 9.90E−18 262 MtN3_slv 135 221 122.5 1.10E−33 263 Cys_Met_Meta_PP 88 460 768.4 3.90E−228 263 Beta_elim_lyase 129 376 −107.7 0.0016 264 PAR1 1 181 469.5 3.60E−138 265 Chal_sti_synt_C 350 493 13.4 0.00012 266 Cyclin_N 43 195 113.1 7.30E−31 267 Pkinase 21 418 193.4 5.00E−55 268 Brix 96 271 216.4 5.60E−62 269 tRNA-synt_2b 81 250 166.9 4.70E−47 269 HGTP_anticodon 402 486 17.1 0.00088 270 Proteasome 38 233 81.4 2.50E−21 271 Ammonium_transp 19 423 597.5 1.10E−176 272 AUX_IAA 8 204 332.3 7.20E−97 273 Lectin_legB 25 215 −14.8 1.60E−09 273 Lectin_legA 236 279 31 3.70E−06 273 Pkinase 355 624 179.3 8.50E−51 273 Pkinase_Tyr 355 624 116.1 9.20E−32 274 PGK 2 395 675.6 3.30E−200 275 Sugar_tr 27 491 416.7 2.90E−122 275 MFS_1 31 467 75.7 1.30E−19 276 Hpt 30 112 54.9 2.30E−13 278 RRN3 37 620 1128.7 0 279 Sugar_tr 89 546 595 6.00E−176 279 MFS_1 93 505 100.6 4.10E−27 280 AP2 25 88 133.6 4.70E−37 281 Pkinase 4 205 28 1.20E−09 282 ADH_N 33 119 53.8 5.30E−13 282 ADH_zinc_N 155 318 43.1 8.50E−10 283 ADH_N 34 149 129.2 1.00E−35 283 ADH_zinc_N 180 315 119.1 1.10E−32 284 ADH_N 40 165 112.8 8.90E−31 284 ADH_zinc_N 196 338 125.2 1.60E−34 285 ADH_N 43 173 105.4 1.50E−28 285 ADH_zinc_N 204 348 112.5 1.10E−30 286 Mov34 23 133 136.1 8.40E−38 287 RRM_1 36 107 101.5 2.20E−27 288 RRM_1 36 107 73 8.20E−19 289 FA_desaturase 54 269 135 1.80E−37 290 Ras 15 176 336.7 3.50E−98 291 SAC3_GANP 24 209 128.9 1.20E−35 292 RNA_pol_L 6 83 75.5 1.50E−19 293 GSHPx 8 117 234.4 2.20E−67 294 FKBP_C 115 214 127.7 3.00E−35 295 Ras 10 171 339 7.10E−99 296 UQ_con 15 148 81.4 2.50E−21 297 Proteasome 28 215 246.5 4.90E−71 298 Ras 14 175 317.4 2.20E−92 299 Ldh_1_N 83 226 247.5 2.40E−71 299 Ldh_1_C 228 394 199.8 5.50E−57 300 Ras 8 209 221.5 1.60E−63 301 ThiF 30 167 −12.5 3.50E−05 303 Sterol_desat 10 215 128.3 1.90E−35 304 Sterol_desat 12 227 195.1 1.50E−55 306 Enolase_N 3 133 227.6 2.40E−65 306 Enolase_C 138 424 567.5 1.10E−167 307 NTP_transferase 4 267 89.5 9.20E−24 308 NAD_binding_2 16 185 −39.1 1.10E−05 308 NAD_Gly3P_dh_N 17 154 −24.6 0.00015 308 F420_oxidored 18 265 341.2 1.60E−99 309 F420_oxidored 4 255 278.2 1.40E−80 310 ADH_N 27 145 115.5 1.40E−31 310 ADH_zinc_N 175 318 138.1 2.10E−38 311 Aminotran_1_2 44 399 178.8 1.20E−50 312 Aldedh 11 476 903.9 6.50E−269 313 NTP_transferase 5 269 52.4 1.40E−13 314 PFK 6 281 515.1 7.10E−152 315 NTP_transferase 10 288 20.8 2.90E−11 316 Aminotran_1_2 114 480 492.5 4.40E−145 317 NTP_transferase 94 349 346.3 4.40E−101 318 Aldedh 13 475 734.7 5.60E−218 319 Aminotran_3 113 448 471.8 7.60E−139 320 Cys_Met_Meta_PP 117 395 −276.6 0.0042 320 Aminotran_1_2 118 471 184.5 2.30E−52 321 Aminotran_1_2 121 483 125.6 1.20E−34 322 DAO 214 489 −32.3 0.0011 322 Pyr_redox_2 214 474 69.5 9.70E−18 322 Pyr_redox 343 433 55.7 1.40E−13 323 PGM_PMM_I 127 272 140.6 3.80E−39 323 PGM_PMM_II 297 407 69.6 8.70E−18 323 PGM_PMM_III 408 528 105.7 1.20E−28 323 PGM_PMM_IV 543 632 55.6 1.50E−13 324 Aminotran_3 192 522 634.1 1.00E−187 325 Biotin_lipoyl 91 164 82.6 1.10E−21 325 E3_binding 198 234 74.5 3.00E−19 325 2-oxoacid_dh 262 493 486.5 2.70E−143 326 Biotin_lipoyl 91 164 79.5 9.50E−21 326 E3_binding 198 234 76.7 6.40E−20 326 2-oxoacid_dh 261 492 483.1 2.90E−142 327 Transaldolase 101 401 580 2.00E−171 328 Biotin_lipoyl 92 165 88.9 1.40E−23 328 E3_binding 201 237 69 1.40E−17 328 2-oxoacid_dh 261 491 478.4 7.90E−141 329 cNMP_binding 103 191 73.7 5.30E−19 330 HI0933_like 90 415 −239.1 0.0006 330 FAD_binding_2 91 401 −113.1 0.0016 330 GIDA 91 420 −208 0.00018 330 DAO 91 353 −32.7 0.0012 330 Pyr_redox_2 91 399 237.8 2.10E−68 330 Pyr_redox 261 354 100.9 3.30E−27 330 Pyr_redox_dim 428 537 164.9 1.90E−46 331 GIDA 94 435 −211.8 0.00032 331 Pyr_redox_2 94 413 217.1 3.40E−62 331 Pyr_redox 271 368 107.5 3.60E−29 331 Pyr_redox_dim 443 552 193.7 3.90E−55 332 FAD_binding_2 99 410 −122.5 0.0042 332 Pyr_redox_2 99 409 275 1.30E−79 332 Pyr_redox 266 362 114.7 2.30E−31 332 Pyr_redox_dim 437 546 202.7 7.40E−58 333 Biotin_lipoyl 92 165 81.4 2.40E−21 333 E3_binding 202 238 68.7 1.60E−17 333 2-oxoacid_dh 261 491 485.1 7.30E−143 334 DUF6 117 242 57.9 3.00E−14 334 DUF250 251 397 196.5 5.70E−56 335 Alpha-amylase 61 489 −62.8 4.70E−06 336 GAF 141 304 86.6 6.80E−23 336 Phytochrome 315 501 33 8.10E−07 336 HWE_HK 520 600 115.8 1.10E−31 336 Response_reg 732 848 36.6 7.80E−08 337 NIR_SIR_ferr 69 137 83 8.50E−22 337 NIR_SIR 169 332 206.4 5.80E−59 337 NIR_SIR_ferr 348 419 75.4 1.50E−19 338 Fer4 9 32 9.4 0.011 338 Fer4 177 202 9.1 0.012 339 PGI 52 541 1099 0 340 Molybdop_Fe4S4 2 68 80.6 4.30E−21 340 Molybdopterin 70 501 390.7 1.90E−114 340 Molydop_binding 627 738 174.9 1.80E−49 341 PGI 55 545 751.6 4.50E−223 342 Iso_dh 28 469 379.1 6.10E−111 343 NIR_SIR_ferr 78 147 71.9 1.80E−18 343 NIR_SIR 179 338 199.5 6.80E−57 343 NIR_SIR_ferr 354 425 67.3 4.50E−17 344 DUF783 27 236 348.6 9.00E−102 346 PA 43 144 89.4 9.50E−24 346 zf-C3HC4 232 273 34.7 3.00E−07 347 Peptidase_C26 13 248 158.9 1.10E−44 348 SURF5 17 143 252 1.10E−72 349 DUF962 7 171 329.8 4.20E−96 350 Cyclin_N 191 318 198.5 1.40E−56 350 Cyclin_C 320 447 173.7 4.00E−49 351 WRKY 237 297 137.6 2.90E−38 352 SBDS 6 244 261.6 1.40E−75 353 DUF167 38 112 82.3 1.40E−21 355 zf-CCCH 2 25 30.5 5.40E−06 356 DIM1 5 139 78.9 1.40E−20 358 Rieske 100 198 68.5 1.90E−17 359 Fe_bilin_red 112 333 416.6 3.20E−122 360 Radical_SAM 123 282 47.3 4.70E−11 361 LEA_4 107 180 55.3 1.80E−13 363 Pribosyltran 92 236 146.3 7.30E−41 364 Rhodanese 254 367 102 1.60E−27 367 DRMBL 248 368 129 1.20E−35 368 MIP 30 251 276.9 3.60E−80 369 EBP 23 219 362.2 7.50E−106 371 CcmH 1 139 16.6 6.30E−09 373 CTP_transf_2 30 170 48.4 2.20E−11 374 AP2 46 109 145.7 1.10E−40 375 HLH 48 97 52.3 1.40E−12 376 Myb_DNA-binding 59 104 58.1 2.50E−14 377 Ham1p_like 12 188 153.2 6.10E−43 378 SRF-TF 9 59 112.2 1.40E−30 378 K-box 74 174 76.9 5.80E−20 379 Response_reg 10 152 75.9 1.20E−19 380 Nuc_sug_transp 105 341 17.6 1.50E−14 381 SRF-TF 9 59 105.7 1.20E−28 381 K-box 70 167 6.3 0.00011 382 E2F_TDP 16 81 111.2 2.60E−30 382 E2F_TDP 151 231 128 2.30E−35 384 RNA_pol_Rpb6 61 114 86.8 5.90E−23 386 Myb_DNA-binding 45 96 41.3 2.90E−09 387 zf-C3HC4 83 122 41.3 2.90E−09 388 zf-C3HC4 42 86 35.1 2.20E−07 389 AUX_IAA 11 234 381.5 1.10E−111 390 Myb_DNA-binding 14 61 49.1 1.30E−11 390 Myb_DNA-binding 67 112 38.4 2.10E−08 391 AP2 49 121 137.7 2.80E−38 391 AP2 151 215 101.8 1.80E−27 392 TCP 56 241 161.1 2.60E−45 393 zf-C3HC4 383 424 43.1 8.30E−10 394 SET 109 238 182.9 7.10E−52 395 zf-C2H2 36 59 18 0.031 396 zf-C3HC4 206 246 34.5 3.40E−07 397 Myb_DNA-binding 26 75 34.3 3.70E−07 397 Myb_DNA-binding 134 181 53.7 5.30E−13 398 bZIP_1 171 234 26.9 6.50E−05 398 bZIP_2 171 221 25.3 0.00019 399 zf-C3HC4 111 152 37.5 4.10E−08 400 WD40 15 51 16.6 0.079 400 WD40 59 95 23.3 0.00075 400 WD40 210 246 16.4 0.093 400 WD40 329 366 21.2 0.0033 401 AP2 15 80 89.1 1.20E−23 402 Arm 35 75 34.2 4.00E−07 402 Arm 297 337 21.5 0.0027 403 Aminotran_3 42 384 494.7 9.80E−146 404 iPGM_N 3 383 716.6 1.60E−212 404 Metalloenzyme 393 512 147.2 3.80E−41 405 DUF231 239 408 227.7 2.30E−65 406 DUF231 231 404 334.6 1.50E−97 407 DUF231 237 405 336.4 4.40E−98 408 NPH3 204 452 364.6 1.40E−106

TABLE 17 Pfam domain accession gathering name number cutoff domain description 2-oxoacid_dh PE00198.12 −112 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ADH_N PF08240.1 −14.5 Alcohol dehydrogenase GroES-like domain ADH_zinc_N PF00107.15 23.8 Zinc-binding dehydrogenase AP2 PF00847.9 0 AP2 domain AUX_IAA PF02309.6 −83 AUX/IAA family Aa_trans PF01490.7 −128.4 Transmembrane amino acid transporter protein Abhydrolase_1 PF00561.9 5.5 alpha/beta hydrolase fold Acyl_transf_1 PF00698.10 −120 Acyl transferase domain Aldedh PF00171.11 −295 Aldehyde dehydrogenase family Aldo_ket_red PF00248.10 −97 Aldo/keto reductase family Alpha-amylase PF00128.11 −93 Alpha amylase, catalytic domain Aminotran_1_2 PF00155.9 −57.5 Aminotransferase class I and II Aminotran_3 PF00202.10 −207.6 Aminotransferase class-III Ammonium_transp PF00909.10 −144 Ammonium Transporter Family Arm PF00514.11 40.1 Armadillo/beta-catenin-like repeat Asn_synthase PF00733.10 −52.8 Asparagine synthase BAG PF02179.5 25 BAG domain BSD PF03909.6 25 BSD domain Beta_elim_lyase PF01212.10 −114.4 Beta-eliminating lyase Biotin_lipoyl PF00364.11 −2.3 Biotin-requiring enzyme Brix PF04427.7 11.4 Brix domain Bromodomain PF00439.13 8.9 Bromodomain C1_4 PF07975.1 25 TFIIH C1-like domain CTP_transf_2 PF01467.15 −11.8 Cytidylyltransferase Catalase PF00199.8 −229 Catalase CcmH PF03918.4 −30.8 Cytochrome C biogenesis protein Chal_sti_synt_C PF02797.5 −6.1 Chalcone and stilbene synthases, C-terminal domain Cyclin_C PF02984.7 −13 Cyclin, C-terminal domain Cyclin_N PF00134.12 −14.7 Cyclin, N-terminal domain Cys_Met_Meta_PP PF01053.9 −278.4 Cys/Met metabolism PLP-dependent enzyme DAO PF01266.11 −36.5 FAD dependent oxidoreductase DIM1 PF02966.6 25 Mitosis protein DIM1 DPBB_1 PF03330.7 30 Rare lipoprotein A (RlpA)-like double-psi beta- barrel DRMBL PF07522.3 25 DNA repair metallo-beta-lactamase DUE167 PF02594.6 25 Uncharacterized ACR, YggU family COG1872 DUF231 PF03005.5 −58 Arabidopsis proteins of unknown function DUF250 PF03151.6 125 Domain of unknown function, DUF250 DUF6 PF00892.9 30 Integral membrane protein DUF6 DUF783 PF05615.2 25 Protein of unknown function (DUF783) DUF962 PF06127.1 25 Protein of unknown function (DUF962) E2F_TDP PF02319.9 17 E2F/DP family winged-helix DNA-binding domain E3_binding PF02817.6 10 e3 binding domain EBP PF05241.1 25 Emopamil binding protein Enolase_C PF00113.11 −34 Enolase, C-terminal TIM barrel domain Enolase_N PF03952.5 −4 Enolase, N-terminal domain F420_oxidored PF03807.5 −34.5 NADP oxidoreductase coenzyme F420- dependent FAD_binding_2 PF00890.13 −124.8 FAD binding domain FA_desaturase PF00487.13 −46 Fatty acid desaturase FKBP_C PF00254.16 −7.6 FKBP-type peptidyl-prolyl cis-trans isomerase FTCD_N PF07837.2 −67.7 Formiminotransferase domain, N-terminal subdomain Fe_bilin_red PF05996.2 25 Ferredoxin-dependent bilin reductase Fer4 PF00037.14 8 4Fe-4S binding domain GAF PF01590.14 23 GAF domain GATase_2 PF00310.10 −106.2 Glutamine amidotransferases class-II GIDA PF01134.11 −226.7 Glucose inhibited division protein A GSHPx PF00255.9 −16 Glutathione peroxidase Gpi16 PF04113.3 −207.8 Gpi16 subunit, GPI transamidase component HGTP_anticodon PF03129.9 −2 Anticodon binding domain HI0933_like PF03486.4 −255.8 HI0933-like protein HLH PF00010.15 8.2 Helix-loop-helix DNA-binding domain HMG_CoA_synt PF01154.7 −230 Hydroxymethylglutaryl-coenzyme A synthase HWE_HK PF07536.4 25 HWE histidine kinase Ham1p_like PF01725.6 −46 Ham1 family HhH-GPD PF00730.13 13.5 HhH-GPD superfamily base excision DNA repair protein Homeobox PF00046.17 −4.1 Homeobox domain Hpt PF01627.11 25 Hpt domain Iso_dh PF00180.9 −97 Isocitrate/isopropylmalate dehydrogenase K-box PF01486.7 0 K-box region LEA_4 PF02987.6 25 Late embryogenesis abundant protein LRRNT_2 PF08263.1 18.6 Leucine rich repeat N-terminal domain LRR_1 PF00560.20 19 Leucine Rich Repeat Ldh_1_C PF02866.6 −13 lactate/malate dehydrogenase, alpha/beta C- terminal domain Ldh_1_N PF00056.11 −31.3 lactate/malate dehydrogenase, NAD binding domain Lectin_legA PF00138.7 19 Legume lectins alpha domain Lectin_legB PF00139.9 −77 Legume lectins beta domain Lipase_GDSL PF00657.11 10.9 GDSL-like Lipase/Acylhydrolase MFS_1 PF07690.4 23.5 Major Facilitator Superfamily MIP PF00230.8 −62 Major intrinsic protein MatE PF01554.8 59.6 MatE Metalloenzyme PF01676.7 −14.4 Metalloenzyme superfamily Methyltransf_11 PF08241.1 17.1 Methyltransferase domain Methyltransf_12 PF08242.1 21.4 Methyltransferase domain Molybdop_Fe4S4 PF04879.5 13.6 Molybdopterin oxidoreductase Fe4S4 domain Molybdopterin PF00384.11 −50 Molybdopterin oxidoreductase Molydop_binding PF01568.10 1.1 Molydopterin dinucleotide binding domain Mov34 PF01398.10 −4 Mov34/MPN/PAD-1 family MtN3_slv PF03083.5 −0.8 MtN3/saliva family Myb_DNA-binding PF00249.18 19.1 Myb-like DNA-binding domain NAD_Gly3P_dh_N PF01210.12 −44 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus NAD_binding_2 PF03446.4 −63.5 NAD binding domain of 6-phosphogluconate dehydrogenase NIR_SIR PF01077.10 −25 Nitrite and sulphite reductase 4Fe-4S domain NIR_SIR_ferr PF03460.5 20 Nitrite/Sulfite reductase ferredoxin-like half domain NPH3 PF03000.4 25 NPH3 family NTP_transferase PF00483.12 −90.5 Nucleotidyl transferase Nuc_sug_transp PF04142.5 −92.4 Nucleotide-sugar transporter PA PF02225.10 13 PA domain PAR1 PF06521.1 25 PAR1 protein PFK PF00365.9 −132 Phosphofructokinase PGI PF00342.8 −168.9 Phosphoglucose isomerase PGK PF00162.8 −95.1 Phosphoglycerate kinase PGM_PMM_I PF02878.5 −37.5 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I PGM_PMM_II PF02879.5 −20 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II PGM_PMM_III PF02880.5 −11 Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III PGM_PMM_IV PF00408.9 −6 Phosphoglucomutase/phosphomannomutase, C-terminal domain PP2C PF00481.10 −44 Protein phosphatase 2C PTR2 PF00854.11 −50 POT family Peptidase_C26 PF07722.2 25 Peptidase C26 Phi_1 PF04674.2 25 Phosphate-induced protein 1 conserved region Phytochrome PF00360.9 11 Phytochrome region Pkinase PF00069.14 −70.8 Protein kinase domain Pkinase_Tyr PF07714.4 65 Protein tyrosine kinase Pollen_allerg_1 PF01357.10 17.2 Pollen allergen Pribosyltran PF00156.14 2 Phosphoribosyl transferase domain Proteasome PF00227.14 −36.7 Proteasome A-type and B-type Pyr_redox PF00070.16 5 Pyridine nucleotide-disulphide oxidoreductase Pyr_redox_2 PF07992.2 −20 Pyridine nucleotide-disulphide oxidoreductase Pyr_redox_dim PF02852.11 −13 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain RNA_pol_L PF01193.11 16.9 RNA polymerase Rpb3/Rpb11 dimerisation domain RNA_pol_Rpb6 PF01192.12 25 RNA polymerase Rpb6 RRM_1 PF00076.10 15.2 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) RRN3 PF05327.1 25 RNA polymerase I specific transcription initiation factor RRN3 Radical_SAM PF04055.8 8.4 Radical SAM superfamily Ras PF00071.11 18 Ras family Response_reg PF00072.11 −14.4 Response regulator receiver domain Rhodanese PF00581.9 25 Rhodanese-like domain Ribosomal_S8e PF01201.11 25 Ribosomal protein S8e Rieske PF00355.15 −7 Rieske [2Fe-2S] domain SAC3_GANP PF03399.5 −15.2 SAC3/GANP/Nin1/mts3/elF-3 p25 family SBDS PF01172.7 −78 Shwachman-Bodian-Diamond syndrome (SBDS) proteins SET PF00856.16 15.8 SET domain SRF-TF PF00319.8 11 SRF-type transcription factor (DNA-binding and dimerisation domain) SURF5 PF06179.2 25 Surfeit locus protein 5 Skp1 PF01466.8 −2 Skp1 family, dimerisation domain Skp1_POZ PF03931.4 14.9 Skp1 family, tetramerisation domain Ssl1 PF04056.4 −151.8 Ssl1-like Sterol_desat PF01598.7 −13 Sterol desaturase Sugar_tr PF00083.12 −85 Sugar (and other) transporter TCP PF03634.3 −38 TCP family transcription factor ThiF PF00899.10 −38.4 ThiF family Transaldolase PF00923.8 −49 Transaldolase UQ_con PF00179.15 −30 Ubiquitin-conjugating enzyme Ubie_methyltran PF01209.8 −117 ubiE/COQ5 methyltransferase family WD40 PF00400.19 21.4 WD domain, G-beta repeat WRKY PF03106.5 25 WRKY DNA-binding domain adh_short PF00106.13 −46.6 short chain dehydrogenase bZIP_1 PF00170.10 16.5 bZIP transcription factor bZIP_2 PF07716.4 15 Basic region leucine zipper cNMP_binding PF00027.17 20.6 Cyclic nucleotide-binding domain iPGM_N PF06415.3 −263.4 BPG-independent PGAM N-terminus (iPGM_N) p450 PF00067.11 −105 Cytochrome P450 tRNA-synt_2b PF00587.14 −40.5 tRNA synthetase class II core domain (G, H, P, S and T) Ubiquitin PF00240.12 19.4 Ubiquitin family zf-A20 PF01754.6 25 A20-like zinc finger zf-AN1 PF01428.6 15 AN1-like Zinc finger zf-B_box PF00643.13 11.1 B-box zinc finger zf-C2H2 PF00096.14 19 Zinc finger, C2H2 type zf-C3HC4 PF00097.12 16.9 Zinc finger, C3HC4 type (RING finger) zf-CCCH PF00642.14 10.7 Zinc finger C-x8-C-x5-C-x3-H type (and similar)

EXAMPLE 5

This example illustrates the construction of plasmids for transferring recombinant DNA into plant cells which can be regenerated into transgenic crop plants of this invention. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. DNA of interest, i.e. each DNA identified in Table 1 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector.

Elements of an exemplary common expression vector, pMON82060 are illustrated in Table 18. The exemplary base vector which is especially useful for corn transformation is illustrated in FIG. 2 and assembled using technology known in the art. The DNA of interest are inserted in a expression vector at the insertion site between the intronI of rice act 1 gene and the termination sequence of PinII gene.

TABLE 18 pMON82060 Coordinates of SEQ ID function name annotation NO: 19249 Agro B-AGRtu.right border Agro right border sequence, essential for 5235-5591 transformation transfer of T-DNA. Gene of P-Os.Act1 Promoter from the rice actin gene act1. 5609-7009 interest plant L-Os.Act1 Leader (first exon) from the rice actin 1 expression gene. cassette I-Os.Act1 First intron and flanking UTR exon sequences from the rice actin 1 gene insertion site T-St.Pis4 The 3′ non-translated region of the 7084-8026 potato proteinase inhibitor II gene which functions to direct polyadenylation of the mRNA Plant P-CaMV.35S CaMV 35S promoter 8075-8398 selectable L-CaMV.35S 5′ UTR from the 35S RNA of CaMV marker CR-Ec.nptII-Tn5 nptII selectable marker that confers 8432-9226 expression resistance to neomycin and kanamycin cassette T-AGRtu.nos A 3′ non-translated region of the 9255-9507 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.. Agro B-AGRtu.left border Agro left border sequence, essential for  39-480 transformation transfer of T-DNA. Maintenance OR-Ec.oriV-RK2 The vegetative origin of replication from 567-963 in E. coli plasmid RK2. CR-Ec.rop Coding region for repressor of primer 2472-2663 from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of replication from 3091-3679 the E. coli plasmid ColE1. P-Ec.aadA-SPC/STR promoter for Tn7 adenylyltransferase 4210-4251 (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 4252-5040 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 adenylyltransferase 5041-5098 (AAD(3″)) gene of E. coli.

Plasmids for use in transformation of soybean are also prepared. Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 19 below. This exemplary soybean transformation base vector illustrated in FIG. 3 was assembled using the technology known in the art. DNA of interest, i.e. each DNA identified in Table 1 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector at the insertion site between the enhanced 35S CaMV promoter and the termination sequence of cotton E6 gene.

TABLE 19 pMON82053 Coordinates of SEQ ID function name annotation NO: 19250 Agro B-AGRtu.left border Agro left border 6144-6585 transforamtion sequence, essential for transfer of T-DNA. Plant P-At.Act7 Promoter from the 6624-7861 selectable arabidopsis actin 7 gene marker L-At.Act7 5′UTR of Arabidopsis expression Act7 gene cassette I-At.Act7 Intron from the Arabidopsis actin7 gene TS-At.ShkG-CTP2 Transit peptide region of 7864-8091 Arabidopsis EPSPS CR-AGRtu.aroA- Synthetic CP4 coding 8092-9459 CP4.nno_At region with dicot preferred codon usage. T-AGRtu.nos A 3′ non-translated region 9466-9718 of the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA. Gene of P-CaMV.35S-enh Promoter for 35S RNA  1-613 interest from CaMV containing a expression duplication of the −90 to −350 cassette region. insertion site T-Gb.E6-3b 3′ untranslated region  688-1002 from the fiber protein E6 gene of sea-island cotton; Agro B-AGRtu.right border Agro right border 1033-1389 transformation sequence, essential for transfer of T-DNA. Maintenance OR-Ec.oriV-RK2 The vegetative origin of 5661-6057 in E. coli replication from plasmid RK2. CR-Ec.rop Coding region for 3961-4152 repressor of primer from the ColE1 plasmid. Expression of this gene product interferes with primer binding at the origin of replication, keeping plasmid copy number low. OR-Ec.ori-ColE1 The minimal origin of 2945-3533 replication from the E. coli plasmid ColE1. P-Ec.aadA-SPC/STR romoter for Tn7 2373-2414 adenylyltransferase (AAD(3″)) CR-Ec.aadA- Coding region for Tn7 1584-2372 SPC/STR adenylyltransferase (AAD(3″)) conferring spectinomycin and streptomycin resistance. T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 1526-1583 adenylyltransferase (AAD(3″)) gene of E. coli.

EXAMPLE 5

This example illustrates monocot plant transformation useful in producing the transgenic plant cells of this invention by transformation of corn. Corn plants of a readily transformable line are grown in the greenhouse and ears harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryos are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryos are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark. Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop. Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals. Transformants are recovered 6 to 8 weeks after initiation of selection.

Plasmid vectors are prepared essentially as described in Example 5 for transforming into corn each of the DNA of interest, i.e. each DNA identified in Table 1 and the DNA for the identified homologous genes, by Agrobacterium-mediated transformation.

For Agrobacterium-mediated transformation of maize callus, immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media, and paromomycin resistant callus identified as containing the recombinant DNA in an expression cassette.

To regenerate transgenic corn plants transgenic callus resulting from transformation is placed on media to initiate shoot development in plantlets which are transferred to potting soil for initial growth in a growth chamber at 26 degrees C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity. The plants are self fertilized and seed is harvested for screening as seed, seedlings or progeny R2 plants or hybrids, e.g. for yield trials in the screens indicated above. Populations of transgenic plants and seeds produced form transgenic plant cells from each transgenic event are screened as described in Example 7 below to identify the members of the population having the enhanced trait.

EXAMPLE 6

This example illustrates dicot plant transformation useful in producing the transgenic plant cells of this invention by transformation of soybean plants. For Agrobacterium mediated transformation, soybean seeds are germinated overnight and the meristem explants excised. The meristems and the explants are placed in a wounding vessel. Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed germination and wounded using sonication. Following wounding, explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots. Trait positive shoots are harvested approximately 6-8 weeks post bombardment and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil. Shoots that remain healthy on selection, but do not produce roots are transferred to non-selective rooting media for an additional two weeks. Roots from any shoots that produce roots off selection are tested for expression of the plant selectable marker before they are transferred to the greenhouse and potted in soil. Populations of transgenic plants and seeds produced form transgenic plant cells from each transgenic event are screened as described in Example 7 below to identify the members of the population having the enhanced trait.

EXAMPLE 7

This example illustrates identification of plant cells of the invention by screening derived plants and seeds for enhanced trait. Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants will not exhibit an enhanced agronomic trait. Populations of transgenic seed and plants prepared in Examples 5 and 6 are screened to identify those transgenic events providing transgenic plant cells with recombinant DNA imparting an enhanced trait. Each population is screened for nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and heat, enhanced level of oil and protein in seed using assays described below. Plant cells having recombinant DNA with each of the genes identified in Table 1 and the identified homologs are identified in plants and seeds with at least one of the enhanced traits.

Selection for Enhanced Nitrogen Use Efficiency

The physiological efficacy of transgenic corn plants (tested as hybrids) can be tested for nitrogen use efficiency (NUE) traits in a high-throughput nitrogen (N) selection method. The collected data are compared to the measurements from wildtype controls using a statistical model to determine if the changes are due to the transgene. Raw data were analyzed by SAS software. Results shown herein are the comparison of transgenic plants relative to the wildtype controls.

(1) Media Preparation for Planting a NUE Protocol

Planting materials used: Metro Mix 200 (vendor: Hummert) Cat. # 10-0325, Scotts Micro Max Nutrients (vendor: Hummert) Cat. # 07-6330, OS 4⅓″×3⅞″ pots (vendor: Hummert) Cat. # 16-1415, OS trays (vendor: Hummert) Cat. # 16-1515, Hoagland's macronutrients solution, Plastic 5″ stakes (vendor: Hummert) yellow Cat. # 49-1569, white Cat. # 49-1505, Labels with numbers indicating material contained in pots. Fill 500 pots to rim with Metro Mix 200 to a weight of ˜140 g/pot. Pots are filled uniformly by using a balancer. Add 0.4 g of Micro Max nutrients to each pot. Stir ingredients with spatula to a depth of 3 inches while preventing material loss.

(2) Planting a NUE Selection in the Greenhouse

(a) Seed Germination—Each pot is lightly altered twice using reverse osmosis purified water. The first watering is scheduled to occur just before planting; and the second watering, after the seed has been planted in the pot. Ten Seeds of each entry (1 seed per pot) are planted to select eight healthy uniform seedlings. Additional wild type controls are planted for use as border rows. Alternatively, 15 seeds of each entry (1 seed per pot) are planted to select 12 healthy uniform seedlings (this larger number of plantings is used for the second, or confirmation, planting). Place pots on each of the 12 shelves in the Conviron growth chamber for seven days. This is done to allow more uniform germination and early seedling growth. The following growth chamber settings are 25° C./day and 22° C./night, 14 hours light and ten hours dark, humidity ˜80%, and light intensity ˜350 μmol/m²/s (at pot level). Watering is done via capillary matting similar to greenhouse benches with duration of ten minutes three times a day.

(b) Seedling transfer—After seven days, the best eight or 12 seedlings for the first or confirmation pass runs, respectively, are chosen and transferred to greenhouse benches. The pots are spaced eight inches apart (center to center) and are positioned on the benches using the spacing patterns printed on the capillary matting. The Vattex matting creates a 384-position grid, randomizing all range, row combinations. Additional pots of controls are placed along the outside of the experimental block to reduce border effects.

Plants are allowed to grow for 28 days under the low N run or for 23 days under the high N run. The macronutrients are dispensed in the form of a macronutrient solution (see composition below) containing precise amounts of N added (2 mM NH₄NO₃ for limiting N selection and 20 mM NH₄NO₃ for high N selection runs). Each pot is manually dispensed 100 ml of nutrient solution three times a week on alternate days starting at eight and ten days after planting for high N and low N runs, respectively. On the day of nutrient application, two 20 min waterings at 05:00 and 13:00 are skipped. The vattex matting should be changed every third run to avoid N accumulation and buildup of root matter. Table 7 shows the amount of nutrients in the nutrient solution for either the low or high nitrogen selection.

TABLE 22 2 mM NH₄NO₃ 20 mM NH₄NO₃ (high (Low Nitrogen Growth Nitrogen Growth Condition, Low N) Condition, High N) Nutrient Stock mL/L mL/L 1 M NH₄N0₃ 2 20 1 M KH₂PO₄ 0.5 0.5 1 M MgSO₄•7H₂O 2 2 1 M CaCl₂ 2.5 2.5 1 M K₂SO₄ 1 1 Note: Adjust pH to 5.6 with HCl or KOH

(c) Harvest Measurements and Data Collection—After 28 days of plant growth for low N runs and 23 days of plant growth for high N runs, the following measurements are taken (phenocodes in parentheses): total shoot fresh mass (g) (SFM) measured by Sartorius electronic balance, V6 leaf chlorophyll measured by Minolta SPAD meter (relative units) (LC), V6 leaf area (cm²) (LA) measured by a Li-Cor leaf area meter, V6 leaf fresh mass (g) (LFM) measured by Sartorius electronic balance, and V6 leaf dry mass (g) (LDM) measured by Sartorius electronic balance. Raw data were analyzed by SAS software. Results shown are the comparison of transgenic plants relative to the wildtype controls.

To take a leaf reading, samples were excised from the V6 leaf. Since chlorophyll meter readings of corn leaves are affected by the part of the leaf and the position of the leaf on the plant that is sampled, SPAD meter readings were done on leaf six of the plants. Three measurements per leaf were taken, of which the first reading was taken from a point one-half the distance between the leaf tip and the collar and halfway from the leaf margin to the midrib while two were taken toward the leaf tip. The measurements were restricted in the area from ½ to ¾ of the total length of the leaf (from the base) with approximately equal spacing between them. The average of the three measurements was taken from the SPAD machine.

Leaf fresh mass is recorded for an excised V6 leaf, the leaf is placed into a paper bag. The paper bags containing the leaves are then placed into a forced air oven at 80° C. for 3 days. After 3 days, the paper bags are removed from the oven and the leaf dry mass measurements are taken.

From the collected data, two derived measurements are made: (1) Leaf chlorophyll area (LCA), which is a product of V6 relative chlorophyll content and its leaf area (relative units). Leaf chlorophyll area=leaf chlorophyll X leaf area. This parameter gives an indication of the spread of chlorophyll over the entire leaf area; (2) specific leaf area (LSA) is calculated as the ratio of V6 leaf area to its dry mass (cm²/g dry mass), a parameter also recognized as a measure of NUE.

Nitrogen Use Field Efficacy Assay

Level I. Transgenic plants provided by the present invention are planted in field without any nitrogen source being applied. Transgenic plants and control plants are grouped by genotype and construct with controls arranged randomly within genotype blocks. Each type of transgenic plants are tested by 3 replications and across 5 locations. Nitrogen levels in the fields are analyzed in early April pre-planting by collecting 30 sample soil cores from 0-24″ and 24 to 48″ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus(P), Potassium(K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations.

Level II. Transgenic plants provided by the present invention are planted in field with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). Liquid 28% or 32% UAN (Urea, Ammonium Nitrogen) are used as the N source and apply by broadcast boom and incorporate with a field cultivator with rear rolling basket in the same direction as intended crop rows. Although there is no N applied to the 0 N treatment the soil should still be disturbed in the same fashion as the treated area. Transgenic plants and control plants are grouped by genotype and construct with controls arranged randomly within genotype blocks. Each type of transgenic plants is tested by 3 replications and across 4 locations. Nitrogen levels in the fields are analyzed in early April pre-planting by collecting 30 sample soil cores from 0-24″ and 24 to 48″ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus(P), Potassium(K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations.

Selection for Increased Yield

Many transgenic plants of this invention exhibit improved yield as compared to a control plant. Improved yield can result from enhanced seed sink potential, i.e. the number and size of endosperm cells or kernels and/or enhanced sink strength, i.e. the rate of starch biosynthesis. Sink potential can be established very early during kernel development, as endosperm cell number and size are determined within the first few days after pollination.

Much of the increase in corn yield of the past several decades has resulted from an increase in planting density. During that period, corn yield has been increasing at a rate of 2.1 bushels/acre/year, but the planting density has increased at a rate of 250 plants/acre/year. A characteristic of modern hybrid corn is the ability of these varieties to be planted at high density. Many studies have shown that a higher than current planting density should result in more biomass production, but current germplasm does not perform, well at these higher densities. One approach to increasing yield is to increase harvest index (HI), the proportion of biomass that is allocated to the kernel compared to total biomass, in high density plantings. Effective yield selection of enhanced yielding transgenic corn events uses hybrid progeny of the transgenic event over multiple locations with plants grown under optimal production management practices, and maximum pest control. A useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons to statistically distinguish yield improvement from natural environmental effects. It is to plant multiple transgenic plants, positive and negative control plants, and pollinator plants in standard plots, for example 2 row plots, 20 feet long by 5 feet wide with 30 inches distance between rows and a 3 foot alley between ranges. Transgenic events can be grouped by recombinant DNA constructs with groups randomly placed in the field. A pollinator plot of a high quality corn line is planted for every two plots to allow open pollination when using male sterile transgenic events. A useful planting density is about 30,000 plants/acre. High planting density is greater than 30,000 plants/acre, preferably about 40,000 plants/acre, more preferably about 42,000 plants/acre, most preferably about 45,000 plants/acre. Transgenic corn plants and soybean plants with each recombinant DNA construct prepared in Examples 5 and 6 are identified as exhibiting at least 5% yield increase as compared to control plants.

Selection for Enhanced Water Use Efficiency (WUE)

Described in this example is a high-throughput method for greenhouse selection of transgenic corn plants to wild type corn plants (tested as inbreds or hybrids) for water use efficiency. This selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment. The hydration status of the shoot tissues following the drought is also measured. The plant height are measured at three time points. The first is taken just prior to the onset drought when the plant is 11 days old, which is the shoot initial height (SIH). The plant height is also measured halfway throughout the drought/re-water regimen, on day 18 after planting, to give rise to the shoot mid-drought height (SMH). Upon the completion of the final drought cycle on day 26 after planting, the shoot portion of the plant is harvested and measured for a final height, which is the shoot wilt height (SWH) and also measured for shoot wilted biomass (SWM). The shoot is placed in water at 40 degree Celsius in the dark. Three days later, the shoot is weighted to give rise to the shoot turgid weight (STM). After drying in an oven for four days, the shoots are weighted for shoot dry biomass (SDM). The shoot average height (SAH) is the mean plant height across the 3 height measurements. The procedure described above may be adjusted for +/−˜one day for each step given the situation.

To correct for slight differences between plants, a size corrected growth value is derived from SIH and SWH. This is the Relative Growth Rate (RGR). Relative Growth Rate (RGR) is calculated for each shoot using the formula [RGR%=(SWH−SIH)/((SWH+SIH)/2)*100]. Relative water content (RWC) is a measurement of how much (%) of the plant was water at harvest. Water Content (RWC) is calculated for each shoot using the formula [RWC%=(SWM−SDM)/(STM−SDM)*100]. Fully watered corn plants of this age run around 98% RWC.

Selection for Growth Under Cold Stress

(1) Cold germination assay—Three sets of seeds are used for the assay. The first set consists of positive transgenic events (F1 hybrid) where the genes of the present invention are expressed in the seed. The second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events. The third set consisted of two cold tolerant and one cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan” (MAESTRO® 80DF Fungicide, Arvesta Corporation, San Francisco, Calif., USA). 0.43 mL Captan is applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the experiment.

Corn kernels are placed embryo side down on blotter paper within an individual cell (8.9×8.9 cm) of a germination tray (54×36 cm). Ten seeds from an event are placed into one cell of the germination tray. Each tray can hold 21 transgenic events and 3 replicates of wildtype (LH244SDms+LH59), which is randomized in a complete block design. For every event there are five replications (five trays). The trays are placed at 9.7 C for 24 days (no light) in a Convrion growth chamber (Conviron Model PGV36, Controlled Environments, Winnipeg, Canada). Two hundred and fifty millilters of deionized water are added to each germination tray. Germination counts are taken 10th, 11th, 12th, 13th, 14th, 17th, 19th, 21st, and 24th day after start date of the experiment. Seeds are considered germinated if the emerged radicle size is 1 cm. From the germination counts germination index is calculated.

The germination index is calculated as per:

Germination index=(⊖([T+1−n _(i) ]*[P _(i) −P _(i-1)]))/T

Where T is the total number of days for which the germination assay is performed. The number of days after planting is defined by n. “i” indicated the number of times the germination had been counted, including the current day. P is the percentage of seeds germinated during any given rating. Statistical differences are calculated between transgenic events and wild type control. After statistical analysis, the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection. The secondary cold screen is conducted in the same manner of the primary selection only increasing the number of repetitions to ten. Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.

(2) Cold Shock assay—The experimental set-up for the cold shock assay is the same as described in the above cold germination assay except seeds were grown in potted media for the cold shock assay.

The desired numbers of 2.5″ square plastic pots are placed on flats (n=32, 4×8). Pots were filled with Metro Mix 200 soil-less media containing 19:6:12 fertilizer (6 lbs/cubic yard) (Metro Mix, Pots and Flat are obtained from Hummert International, Earth City, Mo.). After planting seeds, pots are placed in a growth chamber set at 23° C., relative humidity of 65% with 12 hour day and night photoperiod (300 uE/m2-min). Planted seeds are watered for 20 minute every other day by sub-irrigation and flats were rotated every third day in a growth chamber for growing corn seedlings.

On the 10^(th) day after planting the transgenic positive and wild-type negative (WT) plants are positioned in flats in an alternating pattern. Chlorophyll fluorescence of plants is measured on the 10^(th) day during the dark period of growth by using a PAM-2000 portable fluorometer as per the manufacturer's instructions (Walz, Germany). After chlorophyll measurements, leaf samples from each event are collected for confirming the expression of genes of the present invention. For expression analysis six V1 leaf tips from each selection are randomly harvested. The flats are moved to a growth chamber set at 5° C. All other conditions such as humidity, day/night cycle and light intensity are held constant in the growth chamber. The flats are sub-irrigated every day after transfer to the cold temperature. On the 4^(th) day chlorophyll fluorescence is measured. Plants are transferred to normal growth conditions after six days of cold shock treatment and allowed to recover for the next three days. During this recovery period the length of the V3 leaf is measured on the 1^(st) and 3^(rd) days. After two days of recovery V2 leaf damage is determined visually by estimating percent of green V2 leaf.

Statistical differences in V3 leaf growth, V2 leaf necrosis and fluorescence during pre-shock and cold shock can be used for estimation of cold shock damage on corn plants.

(3) Early seedling growth assay—Three sets of seeds are used for the experiment. The first set consists of positive transgenic events (F1 hybrid) where the genes of the present invention are expressed in the seed. The second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events. The third seed set consists of two cold tolerant and two cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan”, (3a,4,7,a-tetrahydro-2-[(trichloromethyl y)thio]-1H-isoindole-1,3(2H)-dione, Drex Chemical Co. Memphis, Tenn.). Captan (0.43 mL) was applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the experiment.

Seeds are grown in germination paper for the early seedling growth assay. Three 12″×18″ pieces of germination paper (Anchor Paper #SD7606) are used for each entry in the test (three repetitions per transgenic event). The papers are wetted in a solution of 0.5% KNO₃ and 0.1% Thyram.

For each paper fifteen seeds are placed on the line evenly spaced down the length of the paper. The fifteen seeds are positioned on the paper such that the radical would grow downward, for example longer distance to the paper's edge. The wet paper is rolled up starting from one of the short ends. The paper is rolled evenly and tight enough to hold the seeds in place. The roll is secured into place with two large paper clips, one at the top and one at the bottom. The rolls are incubated in a growth chamber at 23° C. for three days in a randomized complete block design within an appropriate container. The chamber is set for 65% humidity with no light cycle. For the cold stress treatment the rolls are then incubated in a growth chamber at 12° C. for twelve days. The chamber is set for 65% humidity with no light cycle.

After the cold treatment the germination papers are unrolled and the seeds that did not germinate are discarded. The lengths of the radicle and coleoptile for each seed are measured through an automated imaging program that automatically collects and processes the images. The imaging program automatically measures the shoot length, root length, and whole seedling length of every individual seedling and then calculates the average of each roll.

After statistical analysis, the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection. The secondary cold selection is conducted in the same manner of the primary selection only increasing the number of repetitions to five. Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.

4. Cold Field Efficacy Trial

This example sets forth a cold field efficacy trial to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers are beginning to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. The cold field efficacy trials are carried out in five locations, including Glyndon Minn., Mason Mich., Monmouth Ill., Dayton Iowa, Mystic Conn. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment, 20 kernels per row and single row per plot. Seeds are planted 1.5 to 2 inch deep into soil to avoid muddy conditions. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.

Seed emergence is defined as the point when the growing shoot breaks the soil surface. The number of emerged seedling in each plot is counted everyday from the day the earliest plot begins to emerge until no significant changes in emergence occur. In addition, for each planting date, the latest date when emergence is 0 in all plots is also recorded. Seedling vigor is also rated at V3-V4 stage before the average of corn plant height reaches 10 inches, with 1=excellent early growth, 5=Average growth and 9=poor growth. Days to 50% emergence, maximum percent emergence and seedling vigor are calculated using SAS software for the data within each location or across all locations.

Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels

This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample. Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan. An NIR calibration for the analytes of interest is used to predict the values of an unknown sample. The NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides a predicted values as well as information on how well the sample fits in the calibration.

Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item # 1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.

TABLE 26 Typical sample(s): Whole grain corn and soybean seeds Analytical time to run method: Less than 0.75 min per sample Total elapsed time per run: 1.5 minute per sample Typical and minimum sample Corn typical: 50 cc; minimum 30 cc size: Soybean typical: 50 cc; minimum 5 cc Typical analytical range: Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.

EXAMPLE 8

This example describes recombinant DNA constructs of the invention, useful for suppressing the expression of a protein identified by Pfam, Catalase, Bromdomain, FFCD_N, MatE, DPBB_(—)1, tRNA-synt_(—)2b, Sugar_tr and MFS_(—)1, DUF6 and DUF250, LEA_(—)4, MIP or DUF231, in a corn or soybean plant, by expressing a sense and an anti-sense fragment of the native DNA encoding the protein, essentially as described in U.S. patent application Ser. No. 11/303,745, incorporated herein by reference. Specific gene suppression constructs are targeted to the native gene in corn and soybean plants that are homologs of the genes encoding the protein with an amino acid sequence of SEQ ID NO:213, 215, 218, 222, 258, 269, 275, 334, 361, 368, and 407.

The constructs include a promoter operably linked to DNA that transcribes to RNA that forms a double stranded RNA in transgenic plant cells for suppressing expression of the protein to provided the enhanced trait in the corn and soybean plants. Populations of transgenic plants and seeds derived from the plant cells are screened to identify those plants exhibiting the enhanced traits associated with suppression of those genes. 

1. A plant cell with stably integrated, recombinant DNA comprising a promoter that is functional in plant cells and that is operably linked to DNA from a plant, bacteria or yeast that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff of 16.9 for amino acid sequence alignment with a protein domain family identified by Pfam name, RNA_pol_L; wherein said plant cell is selected from a population of plant cells with said recombinant DNA by screening plants that are regenerated from plant cells in said population and that express said protein for an enhanced trait as compared to control plants that do not have said recombinant DNA; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 2. A plant cell with stably integrated, recombinant DNA comprising a promoter that is functional in plant cells and that is operably linked to DNA from a plant, bacteria or yeast that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names consisting of 2-oxoacid_dh, ADH_N, ADH_zinc_N, AP2, AUX_IAA, Aa_trans, Abhydrolase_(—)1, Acyl_transf_(—)1, Aldedh, Aldo_ket_red, Alpha-amylase, Aminotran_(—)1_(—)2, Aminotran_(—)3, Ammonium_transp, Arm, Asn_synthase, BAG, BSD, Beta_elim_lyase, Biotin_lipoyl, Brix, Bromodomain, C1_(—)4, CTP_transf_(—)2, Catalase, CcmH, Chal_sti_synt_C, Cyclin_C, Cyclin_N, Cys_Met_Meta_PP, DAO, DIM1, DPBB_(—)1, DRMBL, DUF167, DUF231, DUF250, DUF6, DUF783, DUF962, E2F_TDP, E3_binding, EBP, Enolase_C, Enolase_N, F420_oxidored, FAD_binding_(—)2, FA_desaturase, FKBP_C, FTCD_N, Fe_bilin_red, Fer4, GAF, GATase_(—)2, GIDA, GSHPx, Gpi16, HGTP_anticodon, HI0933_like, HLH, HMG_CoA_synt, HWE_HK, Hamlp_like, HhH-GPD, Homeobox, Hpt, Iso_dh, K-box, LEA_(—)4, LRRNT_(—)2, LRR_(—)1, Ldh_(—)1_C, Ldh_(—)1_N, Lectin_legA, Lectin_legB, Lipase_GDSL, MFS_(—)1, MIP, MatE, Metalloenzyme, Methyltransf_(—)1, Methyltransf_(—)12, Molybdop_Fe4S4, Molybdopterin, Molydop_binding, Mov34, MtN3_slv, Myb_DNA-binding, NAD_Gly3P_dh_N, NAD_binding_(—)2, NIR_SIR, NIR_SIR_ferr, NPH3, NTP_transferase, Nuc_sug_transp, PA, PAR1, PFK, PGI, PGK, PGM_PMM_I, PGM_PMM_II, PGM_PMM_III, PGM_PMM_IV, PP2C, PTR2, Peptidase_C26, Phi_(—)1, Phytochrome, Pkinase, Pkinase_Tyr, Pollen_allerg_(—)1, Pribosyltran, Proteasome, Pyr_redox, Pyr_redox_(—)2, Pyr_redox_dim, RNA_pol_L, RNA_pol_Rpb6, RRM_(—)1, RRN3, Radical_SAM, Ras, Response_reg, Rhodanese, Ribosomal_S8e, Rieske, SAC3_GANP, SBDS, SET, SRF-TF, SURF5, Skp1, Skp1_POZ, Ssl1, Sterol_desat, Sugar_tr, TCP, ThiF, Transaldolase, UQ_con, Ubie_methyltran, WD40, WRKY, adh_short, bZIP_(—)1, bZIP_(—)2, cNMP_binding, iPGM_N, p450, tRNA-synt_(—)2b, ubiquitin, zf-A20, zf-AN1, zf-B_box, zf-C₂H₂, zf-C3HC4, zf-CCCH wherein the Pfam gathering cuttoff for said protein domain families is stated in Table 16; wherein said plant cell is selected from a population of plant cells with said recombinant DNA by screening plants that are regenerated from plant cells in said population and that express said protein for an enhanced trait as compared to control plants that do not have said recombinant DNA; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
 3. A plant cell of claim 2 wherein said protein has an amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of consensus amino acid sequences consisting of the consensus amino acid sequence constructed for SEQ ID NO: 205 and homologs thereof listed in Table 2 through the consensus amino acid sequence constructed for SEQ ID NO:408 and homologs thereof listed in Table
 2. 4. A plant cell of claim 2 wherein said protein is selected from the group of proteins identified in Table
 1. 5. A plant cell of claim 2 further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
 6. A plant cell of claim 5 wherein the agent of said herbicide is a glyphosate, dicamba, or glufosinate compound.
 7. A transgenic plant comprising a plurality of the plant cells of claim
 2. 8. A transgenic plant of claim 7 which is homozygous for said recombinant DNA.
 9. A transgenic seed comprising a plurality of the plant cell of claim
 2. 10. A transgenic seed of claim 9 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
 11. Non-natural, transgenic corn seed of claim 10 wherein said seed can produce corn plants that are resistant to disease from the Mal de Rio Cuarto virus or the Puccina sorghi fungus or both.
 12. A transgenic pollen grain comprising a haploid derivative of a plant cell of claim
 2. 13. A method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA from a plant, bacteria or yeast that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names consisting of 2-oxoacid_dh, ADH_N, ADH_zinc_N, AP2, AUX_IAA, Aa_trans, Abhydrolase_(—)1, Acyl_transf_(—)1, Aldedh, Aldo_ket_red, Alpha-amylase, Aminotran_(—)1_(—)2, Aminotran_(—)3, Ammonium_transp, Arm, Asn_synthase, BAG, BSD, Beta_elim_lyase, Biotin_lipoyl, Brix, Bromodomain, C1_(—)4, CTP_transf_(—)2, Catalase, CcmH, Chal_sti_synt_C, Cyclin_C, Cyclin_N, Cys_Met_Meta_PP, DAO, DIM1, DPBB_(—)1, DRMBL, DUF167, DUF231, DUF250, DUF6, DUF783, DUF962, E2F_TDP, E3_binding, EBP, Enolase_C, Enolase_N, F420_oxidored, FAD_binding_(—)2, FA_desaturase, FKBP_C, FTCD_N, Fe_bilin_red, Fer4, GAF, GATase_(—)2, GIDA, GSHPx, Gpi16, HGTP_anticodon, HI0933_like, HLH, HMG_CoA_synt, HWE_HK, Hamlp_like, HhH-GPD, Homeobox, Hpt, Iso_dh, K-box, LEA_(—)4, LRRNT_(—)2, LRR_(—)1, Ldh_(—)1_C, Ldh_(—)1_N. Lectin_legA, Lectin_legB, Lipase_GDSL, MFS_(—)1, MIP, MatE, Metalloenzyme, Methyltransf_(—)11, Methyltransf_(—)12, Molybdop_Fe4S4, Molybdopterin, Molydop_binding, Mov34, MtN3_slv, Myb_DNA-binding, NAD_Gly3P_dh_N, NAD_binding_(—)2, NIR_SIR, NIR_SIR_ferr, NPH3, NTP_transferase, Nuc_sug_transp, PA, PAR1, PFK, PGI, PGK, PGM_PMM_I, PGM_PMM_II, PGM_PMM_III, PGM_PMM_IV, PP2C, PTR2, Peptidase_C26, Phi_(—)1, Phytochrome, Pkinase, Pkinase_Tyr, Pollen_allerg_(—)1, Pribosyltran, Proteasome, Pyr_redox, Pyr_redox_(—)2, Pyr_redox_dim, RNA_pol_L, RNA_pol_Rpb6, RRM_(—)1, RRN3, Radical_SAM, Ras, Response_reg, Rhodanese, Ribosomal_S8e, Rieske, SAC3_GANP, SBDS, SET, SRF-TF, SURF5, Skp1, Skp1_POZ, Ssl1, Sterol_desat, Sugar_tr, TCP, ThiF, Transaldolase, UQ_con, Ubie_methyltran, WD40, WRKY, adh_short, bZIP_(—)1, bZIP_(—)2, cNMP_binding, iPGM_N, p450, tRNA-synt_(—)2b, ubiquitin, zf-A20, zf-AN1, zf-B_box, zf-C₂H₂, zf-C3HC4, zf-CCCH; wherein the gathering cutoff for said protein domain families is stated in Table 16; and wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil, said method for manufacturing said seed comprising: (a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not express the recombinant DNA, (b) selecting from said population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants, (c) verifying that said recombinant DNA is stably integrated in said selected plants, (d) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by nucleotides in a sequence of one of SEQ ID NO:205-408; and (e) collecting seed from a selected plant.
 14. A method of claim 13 wherein plants in said population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells, and wherein said selecting is effected by treating said population with said herbicide.
 15. A method of claim 14 wherein said herbicide comprises a glyphosate, dicamba, or glufosinate compound.
 16. A method of claim 13 wherein said selecting is effected by identifying plants with said enhanced trait.
 17. A method of claim 14 wherein said seed is corn, soybean, cotton, alfalfa, wheat or rice seed.
 18. A method of producing hybrid corn seed comprising: (a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA that encodes a protein having at least one domain of amino acids in a sequence that exceeds the Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by a Pfam name in the group of Pfam names consisting of 2-oxoacid_dh, ADH_N, ADH_zinc_N, AP2, AUX_IAA, Aa_trans, Abhydrolase_(—)1, Acyl_transf_(—)1, Aldedh, Aldo_ket_red, Alpha-amylase, Aminotran_(—)1_(—)2, Aminotran_(—)3, Ammonium_transp, Arm, Asn_synthase, BAG, BSD, Beta_elim_lyase, Biotin_lipoyl, Brix, Bromodomain, C1_(—)4, CTP_transf_(—)2, Catalase, CcmH, Chal_sti_synt_C, Cyclin_C, Cyclin_N, Cys_Met_Meta_PP, DAO, DIM1, DPBB_(—)1, DRMBL, DUF167, DUF231, DUF250, DUF6, DUF783, DUF962, E2F_TDP, E3_binding, EBP, Enolase_C, Enolase_N, F420_oxidored, FAD_binding_(—)2, FA_desaturase, FKBP_C, FTCD_N, Fe_bilin_red, Fer4, GAF, GATase_(—)2, GIDA, GSHPx, Gpi16, HGTP_anticodon, HI0933_like, HLH, HMG_CoA_synt, HWE_HK, Hamlp_like, HhH-GPD, Homeobox, Hpt, Iso_dh, K-box, LEA_(—)4, LRRNT_(—)2, LRR_(—)1, Ldh_(—)1_C, Ldh_(—)1_N, Lectin_legA, Lectin_legB, Lipase_GDSL, MFS_(—)1, MIP, MatE, Metalloenzyme, Methyltransf_(—)11, Methyltransf_(—)12, Molybdop_Fe4S4, Molybdopterin, Molydop_binding, Mov34, MtN3_slv, Myb_DNA-binding, NAD_Gly3P_dh_N, NAD_binding_(—)2, NIR_SIR, NIR_SIR_ferr, NPH3, NTP_transferase, Nuc_sug_transp, PA, PAR1, PFK, PGI, PGK, PGM_PMM_I, PGM_PMM_II, PGM_PMM_II, PGM_PMM_IV, PP2C, PTR2, Peptidase_C26, Phi_(—)1, Phytochrome, Pkinase, Pkinase_Tyr, Pollen_allerg_(—)1, Pribosyltran, Proteasome, Pyr_redox, Pyr_redox_(—)2, Pyr_redox_dim, RNA_pol_L, RNA_pol_Rpb6, RRM_(—)1, RRN3, Radical_SAM, Ras, Response_reg, Rhodanese, Ribosomal_S8e, Rieske, SAC3_GANP, SBDS, SET, SRF-TF, SURF5, Skp1, Skp1_POZ, Ssl1, Sterol_desat, Sugar_tr, TCP, ThiF, Transaldolase, UQ_con, Ubie_methyltran, WD40, WRKY, adh_short, bZIP_(—)1, bZIP_(—)2, cNMP_binding, iPGM_N, p450, tRNA-synt_(—)2b, ubiquitin, zf-A20, zf-AN1, zf-B_box, zf-C₂H₂, zf-C3HC4, zf-CCCH; wherein the gathering cuttoff for said protein domain families is stated in Table 16; (b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; (c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; (d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; (e) repeating steps (c) and (d) at least once to produce an inbred corn line; (f) crossing said inbred corn line with a second corn line to produce hybrid seed.
 19. The method of selecting a plant comprising cells of claim 1 or 2 wherein an immunoreactive antibody is used to detect the presence of said protein in seed or plant tissue.
 20. Anti-counterfeit milled seed having, as an indication of origin, a plant cell of claim 1 or
 2. 21. A method of growing a corn, cotton or soybean crop without irrigation water comprising planting seed having plant cells of claim 1 or 2 which are selected for enhanced water use efficiency.
 22. A method of claim 21 comprising providing up to 300 millimeters of ground water during the production of said crop.
 22. A method of growing a corn, cotton or soybean crop without added nitrogen fertilizer comprising planting seed having plant cells of claim 1 or 2 which are selected for enhanced nitrogen use efficiency.
 23. A plant cell with stably integrated, recombinant DNA that is to suppress the level of an endogenous protein having at least one domain of amino acids in a sequence that exceeds that Pfam gathering cutoff for amino acid sequence alignment with a protein domain family identified by Pfam name in the group of Pfam names consisting of Catalase, Bromodomain, FTCD_N, MatE, DPBB_(—)1, Pollen_allerg_(—)1, tRNA-synt_(—)2b, HGTP_anticodon, Sugar_tr, MFS_(—)1, DUF6, DUF250, LEA_(—)4, MIP, and DUF231 wherein the Pfam gathering cutoff for said protein domain families is stated in Table 16; wherein said plant cells is selected from a population of plant cells with said recombinant DNA by screening plants that are regenerated from plant cells in said population and that the level of said protein is suppressed for an enhanced trait as compared to control plants that do not have said recombinant DNA; and wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. 